Genetic Mutation Overview

                 
Hello All,
Several months ago I posted this and then removed it. I have decided to post it once again to demonstrate the need for clinical diagnosing and Whole Genome Sequencing (WES) (DNA/Genetic Testing) if possible.

(Added January 12, 2017...Discussion including testing done 'overseas' refers to the testing in Germany that was previously done for people trying to get a diagnosis of PP. About two years ago the testing was stopped after Dr Lehman-Horne retired due to illness and funding was cut. I am not sure how many people were led to believe they did not have PP due to the biased and limited testing. This has created no end of problems for those attempting to get diagnosed and the misconceptions by doctors still relying on biased and limited test results. Only about 50% of genetic mutations for the various forms of PP have actually been found to date. That means about 50% of all people with PP will have test results possibly find a mutation. This number drops significantly in the testing is limited and/or biased.)
                

Genetic Mutation Overview for Susan Q. Knittle-Hunter
From:

 Ancestry DNA Ethnic DNA Testing

Through:

GEDmatch DNA and Genealogy Research

Rare SNP (Minor Allele) Search Utility

May 2014

(This is in a smaller font so the charts can post correctly)

According to the American Heart Association, ”The approach to genetic studies of complex traits entails candidate gene or genome-wide association studies. Genome-wide association studies provide an unbiased survey of the effects of common genetic variants (common disease–common variant hypothesis).”

“Based on today’s knowledge, only 1% of the human genome is transcribed into mRNA and translated into proteins. An additional 0.5% serves as a template for noncoding RNA and the regulatory regions that control gene expression.⁵ The functions of the remaining 98.5% of the genome including functional conserved noncoding elements, which comprise at least 6% of the genome,⁶ remain unknown. Hence, this large segment of the genome is referred to as the dark matter of the genome.”

http://circres.ahajournals.org/content/108/10/1252.full

This would indicate that genome-wide genetic testing would be the best way to test for the various forms of Periodic Paralysis (PP), but since only 1% of human genome has actually been transcribed, it also indicates why less that half of those tested get negative results. The research labs run testing only for the tests requested by the doctors ordering them. If testing for only one form of Periodic Paralysis is requested, that is all that will be checked. If blood is sent overseas for testing for Periodic Paralysis, only the known mutations are searched for and they are either found or not found. There is no research done on what mutations on the same gene in the same exons or locations mean nor do they report those findings on the results if they are found in the denial letter sent. This is definite “bias” in the testing. One is left to believe there is no reason for their symptoms and to wonder about their own sanity. An individual’s doctors, not understanding the above information, believe that the person does not have Periodic Paralysis.

 I know that the testing overseas does not test for every known variant of PP. How do I know? Because I have a copy of the letter from them telling me which genes were tested. I also have a copy of my own genetic mutation make-up from Ancestry, which includes all of my known genetic mutations.

Overseas, they sequenced:  KCNJ2 (ATS), CACNA1S (4, 11, 21,30), SCN4A (exons 5, 6, 9, 12, 13, 14, 18, 19, 21, 22, 23, 2. These are not the only gene mutations associated with the many forms of Periodic Paralysis 4), Kir2.1, (potassium channels), Nav1.4 (sodium channels), Cav1.1 (calcium channels).

It was added in the letter that my “type of channelopathy is caused by either a mutation located in an exon that was “not” part of the screening program or by a mutation in a new gene still to be indentified.”  That is exactly the case.

SCN4A 

Searching my own DNA mutations and researching as I went along (not an easy task it has taken months of research and study), I discovered that I have five mutations in the SCN4A gene as follows. Three of the mutations were found on exon 8 which was not included in the testing and the others were not mentioned to me, though they were found in SCN4A which is the “sodium channel, voltage-gated, type IV, alpha subunit” and “mutations in this gene have been linked to several myotonia and periodic paralysis disorders”:

Mutation shown in red

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs16947296	17	59397269	aG	2.22617	SCN4A	Exon 8
rs2008896	17	59396947	aG	2.58377	SCN4A	Exon 8 & 9
rs7218917	17	59399287	Ag	3.30962	SCN4A	Exon 6
Rs2302236	17	59402199	Ag	12.087	SCN4A	Exon 5
rs11079516	17	59396573	Ag	13.5948	SCN4A	Exon 8 & 9

All five mutations are identified as *603967.

*603967 =
SODIUM CHANNEL, VOLTAGE-GATED, TYPE IV, ALPHA SUBUNIT; SCN4A
Alternative titles; symbols
NAV1.4
HGNC Approved Gene Symbol: SCN4A
Location	Phenotype	Phenotype MIM number
17q23.3	Hyperkalemic periodic paralysis, type 2	170500
	Hypokalemic periodic paralysis, type 2	613345
	Myasthenic syndrome, acetazolamide-responsive	614198
	Myotonia congenita, atypical, acetazolamide-responsive	608390
	Paramyotonia congenita	168300
Cytogenetic location: 17q23.3     Genomic coordinates (GRCh37): 17:62,015,913 - 62,066,875 (from NCBI) http://omim.org/entry/603967

SCN4A is a Voltage-gated sodium channel.
SCN4A sodium channel, voltage-gated, type IV, alpha subunit

Also known as: HYPP; SkM1; HYKPP; NAC1A; HOKPP2; Nav1.4; Na(V)1.4

The mutations above are directly related to:

“Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. It is expressed in skeletal muscle, and mutations in this gene have been linked to several myotonia and periodic paralysis disorders. [provided by RefSeq, Jul 2008]”

http://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&dopt=full_report&list_uids=6329

The following are the mutations I discovered. Each one is a definite mutation, which causes Paramyotonia Congenita (PMC) a form of Periodic Paralysis. I have a combination of the three of them:

08

c.1167T>C c.703+55C>T, c.864C>T,

Tyr389Tyr

SCN4A_00012

DNA

SEQ

-

-

paramyotonia congenita (OMIM168300)

http://chromium.liacs.nl/LOVD2/variants.php?select_db=SCN4A&action=search_all&search_Variant%2FDNA=c.1167T%3EC

05i	c.703+55C>T	-	r.(?)	p.(=)	(LDGA)
06	c.864C>T	-	r.(?)	p.(Asn288Asn)	(LDGA)
08	c.1167T>C	Tyr389Tyr	r.(?)	p.(=)	(LDGA)

According to Ptácek, LJ, et al., “Mutations 1, 4, 6, 7, 8, and 18 are associated with PAM; mutations 2, 9, 12, 13, 14, 15, and 16 are associated with PC; and mutations 3, 5, 10, 11, 17, and 19 are associated with HyperKPP.”  And some double mutations on exon 5 are now known to cause Hyperkalemic Periodic Paralysis.

http://www.jci.org/articles/view/9654

http://chromium.liacs.nl/LOVD2/variants.php?select_db=SCN4A&action=view_all&order=Variant/DNA,ASC&hide_col=&show_col=&limit=1000

                       

As listed above for SCN4A, exon 8 was not tested in the overseas testing. These mutations were not seen. I am not sure why they did not show up in exon 5 and 6, or if they were disregarded.  Apparently, by themselves, each of these does not cause it, but the combination does. So it would not be found based on their testing.

I also discovered that one of those mutations above is responsible for what is called "enhanced slow inactivation.” This is related to how long the episode of paralysis/weakness may last. If one has "enhanced slow inactivation", it causes their episodes to last longer. My research also led me to the knowledge that a lower pH will help shorten the length of weakness or prevent it.

There is no doubt that I have Paramyotonia Congenita. The specific mutations I have at exons 6 and 8 have been found to be associated with PMC and research indicates that mutations at exon 5 are associated with Hyperkalemic Periodic Paralysis.

 KCNJ5

 With the discovery of a new journal article indicating that mutations at the KCNJ5 gene on Chromosome 11 is now linked to Andersen-Tawil Syndrome, I searched through my DNA data. Much to my surprise I discovered I have three mutations on KCNJ5:

Mutation shown in red

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs7118824	11	128287188	gT	17.1178	KCNJ5	Exon 2
rs1317470	11	128287424	aG	17.6794	KCNJ5	Exon 2
rs11221503	11	128277662	cT	19.5168	C11orf45	KCNJ5 Ex 2&3

“CONCLUSIONS: Our findings indicate that rs6590357 and rs7118824 [G810T] in KCNJ5 are associated with early-onset lone AF in Caucasians.” http://www.ncbi.nlm.nih.gov/pubmed/21555883 “The risk of stroke is increased fivefold in individuals with AF. The degree of increased risk may be substantial, depending on the presence of additional risk factors (such as high blood pressure).” http://en.wikipedia.org/wiki/Atrial_fibrillation This would indicate that I have the mutation responsible for early onset Atrial Fibrillation.  It has obviously been aggravated by the potassium shifting from the Periodic Paralysis. This has been evident since my young adulthood. It is now probably responsible for the TIAs that I have experienced in the past few months. The following is also related to these mutations: The C11orf45 indicates 3 mutations within the sequence. All three mutations are identified as *600734. *600734
POTASSIUM CHANNEL, INWARDLY RECTIFYING, SUBFAMILY J, MEMBER 5; KCNJ5
Alternative titles; symbols
CARDIAC INWARD RECTIFIER; CIR G PROTEIN-ACTIVATED INWARDLY RECTIFYING POTASSIUM CHANNEL 4; GIRK4 INWARDLY RECTIFYING POTASSIUM CHANNEL KIR3.4 KATP1
HGNC Approved Gene Symbol: KCNJ5
Cytogenetic location: 11q24.3   Genomic coordinates (GRCh37): 11:128,761,312 - 128,791,059 (from NCBI) http://omim.org/entry/600734 Location Phenotype Phenotype MIM number 11q24.3 Long QT syndrome 13 613485
#613485
LONG QT SYNDROME 13; LQT13
Phenotype-Gene Relationships Location Phenotype Phenotype MIM number Gene/Locus Gene/Locus MIM number 11q24.3 Long QT syndrome 13 613485 KCNJ5 600734
600734
TEXT
A number sign (#) is used with this entry because long QT syndrome-13 is caused by heterozygous mutation in the KCNJ5 gene (600734) on chromosome 11q24. http://omim.org/entry/613485

According toYosuke Kokunai, MD, PhD, et al…”We identified a mutation in the KCNJ5 gene, which encodes the G-protein–activated inwardly rectifying potassium channel 4 (Kir3.4).
We propose that KCNJ5 is a second gene causing Andersen–Tawil syndrome. The inhibitory effects of mutant Kir3.4 on inwardly rectifying potassium channels may account for the clinical presentation in both skeletal and heart muscles.”
http://www.neurology.org/content/early/2014/02/26/WNL.0000000000000239.abstract
 Mutations in Kv1.4 and Kir3.4 channels are also related to potassium and pH balance.

http://www.ncbi.nlm.nih.gov/pubmed/15454439

The information above regarding mutations at SCN4A indicates I have issues with sodium Channel, voltage-gated, type IV, alpha subnit and mutations KCNJ5 indicate strong evidence that I have a variant of Andersen-Tawil Syndrome. But I was not told of these mutations and their implications. My researches lead me to even more mutations in my genes related to calcium channels also involved with potassium shifting, periodic paralysis and pH balance.

CACNA1C

I have mutations on the CACNA1C gene, which are related to the SCN5A gene. The CACNA1C gene was not tested in the overseas research. New information has been published to relate mutations on the CACNAIC gene, also known as Cav1.1, is the first calcium channel related to Normokalemic Periodic Paralysis. I have 24 mutations on this gene!

Mutation shown in red

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs2283284	12	2104022	cT	2.5786	CACNA1C
rs2270371	12	2656118	Ag	4.48034	CACNA1C
rs12230535	12	2117693	aG	6.29314	CACNA1C
rs2302727	12	2644862	Ac	6.77245	CACNA1C
rs2239126	12	2622948	Ag	7.29738	CACNA1C
rs215976	12	2564899	cT	8.81847	CACNA1C
rs4765970	12	2662922	aG	9.31559	CACNA1C
rs11831557	12	2385250	Gt	9.37356	CACNA1C
rs7957163	12	2675893	Ac	9.68454	CACNA1C
rs3794288	12	2659482	aG	9.96197	CACNA1C
rs2238096	12	2620174	aC	10.311	CACNA1C
rs2239093	12	2479823	Ag	11.1857	CACNA1C
rs216009	12	2592794	CC	11.5033	CACNA1C
rs1076346	12	2424539	Ct	11.8242	CACNA1C
rs16929471	12	2472004	Ag	13.1292	CACNA1C
rs216013	12	2599893	GG	16.2705	CACNA1C
rs11831085	12	2385119	aG	16.3592	CACNA1C
rs2370515	12	2381423	Ag	16.4472	CACNA1C
rs10848666	12	2479535	Ag	16.4819	CACNA1C
rs1076390	12	2602980	AA	16.4989	CACNA1C
rs2370602	12	2546944	Ct	16.5967	CACNA1C
rs7301013	12	2378832	aG	17.0857	CACNA1C
rs98545	12	2607556	TT	17.3897	CACNA1C
rs215986	12	2580141	cT	19.9388	CACNA1C

 According to Lehman-Horn F. et al, “This study shows for the first time that functional characterization of omega pore currents is possible using a cultured cell line expressing mutant Ca(v)1.1 channels. Likewise, it is the first calcium channel mutation for complicated normokalaemic periodic paralysis.” http://www.ncbi.nlm.nih.gov/pubmed/24240197/

*114205

CALCIUM CHANNEL, VOLTAGE-DEPENDENT, L TYPE, ALPHA-1C SUBUNIT; CACNA1C, also known as Long QT 8

Alternative titles; symbols

CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 1, CARDIAC MUSCLE; CACNL1A1 CCHL1A1 CaV1.2 CALCIUM CHANNEL, CARDIAC DIHYDROPYRIDINE-SENSITIVE, ALPHA-1 SUBUNIT DHPR, ALPHA-1 SUBUNIT CACH2

HGNC Approved Gene Symbol: CACNA1C

Cytogenetic location: 12p13.33     Genomic coordinates (GRCh37): 12:2,079,951 - 2,807,114 (from NCBI) http://omim.org/entry/114205

CACNA1C is an important paralog of the gene SCN5A. This means the genes are related by duplication and they evolve into a new functions.

http://homepage.usask.ca/~ctl271/857/def_homolog.shtml

http://www.genecards.org/cgi-bin/carddisp.pl?gene=CACNA1C

KCNJ16 and KCNJ2

Although I do not have KCNJ2 (ATS) mutations, I have mutations at KCNJ16 on chromosome 17 at 17q23.1-q24.2. KCNJ16 and KCNJ2 (ATS) are separated by only 34 kb, which is extremely close and there is interaction and interplay between these two genes.

http://www.omim.org/entry/600681

Mutation shown in red

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs8072022	17	65606151	Ct	9.80244	KCNJ16

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs2836251	21	38555062	Gt	18.8342	KCNJ15

***http://www.ncbi.nlm.nih.gov/clinvar/RCV000051047/

There are more mutations related to the above mutations, which I also have. But will not add them to this list.

KCNQ1

I also know that for sure I have the mutation for Long QT 1:

Mutation shown in red

RSID	Chr	Position (B36)	Genotype	%Occurrence	Gene	Matching Origins
rs12418076	11	2645676	Ct	8.77465	KCNQ1
rs231887	11	2695756	cT	12.6968	KCNQ1
rs9666604	11	2654171	aG	12.7112	KCNQ1
rs12576239	11	2458895	cT	14.8241	KCNQ1
rs1057128	11	2753813	Ag	19.2399	KCNQ1

http://www.ncbi.nlm.nih.gov/pubmed/24190995/

KCNQ1 : rs1057128 c.1638G>A (p.Ser546=) AND AllHighlyPenetrant

"AllHighlyPenetrant"
Term used to represent disorders for which a pathogenic allele would be expected to be expressed as the disorder."

This means if you have this mutation...you have a very high chance of having or developing the disease.

So it would seem I have PMC and Long QT 1 and the possibility of HyperPP and/or Normo PP and/or ATS.

No wonder I am sick!!

The reason I am sharing all of this is to let you know that the testing done on one or two genes, ordered by your doctor, is useless and the testing done overseas is not testing for every possibility. Many gene mutations work together to create illness/disease in our bodies. This is explained below.

”SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of non-coding RNA. Gene expression affected by this type of SNP is referred to as an eSNP (expression SNP) and may be upstream or downstream from the gene.

Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also critical for personalized medicine.^[5] However, their greatest importance in biomedical research is for comparing regions of the genome between cohorts (such as with matched cohorts with and without a disease) in genome-wide association studies.

SNPs are usually biallelic and thus easily assayed.^[6] A single SNP may cause a Mendelian disease. For complex diseases, SNPs do not usually function individually, rather, they work in coordination with other SNPs to manifest a disease condition as has been seen in Osteoporosis.^[7]”

http://en.wikipedia.org/wiki/Single-nucleotide_polymorphism

Unless someone can take to time, and hours, days, weeks and months...even years of research like I am doing for myself...these things can and will be missed and overlooked.

Based on all of the above information, we need to be diagnosed clinically, based on our symptoms and whole genome testing needs to be done with the hope that whoever is doing the research understands the workings among and between the genes.

I would like to conclude this article with another article posted recently:
Hello All,

Today one of our extremely conscientious members, who is always researching about all aspects of Periodic Paralysis and sharing the articles she finds with us, posted an article about DNA and genetic testing. The article, which was thirty-five pages long, was filled with a great deal of technical information. I know a lot great deal about DNA and genetic testing from my own study, but it is always very difficult for me to understand when I do read that kind of article. This article was one of those, but as I was reading along, something jumped off the page to me. The following is my response to the article:

Thank you for sharing this with us. As usual when I read about DNA genetic testing I get confused and lost.  Although I feel I understand quite a bit about it, the articles always seem to be difficult to understand. However, in this article, one thing popped out to me; the following statement:

"For the great majority of diseases there is extensive allelic heterogeneity, and genetic testing requires a search for any mutation anywhere within or near the relevant gene. The biggest current problem in laboratory genetic diagnosis is the lack of any quick, cheap and reliable method for doing this."

This is exactly what I have been trying to say for quite awhile about our testing for Periodic Paralysis....."GENETIC TESTING REQUIRES A SEARCH FOR ANY MUTATION ANYWHERE WITHIN OR NEAR THE RELEVANT GENE"!!!!!!!!!!
 
That is what has been missing for most of us whether our genetic testing was done in Germany, or from a doctor's orders somewhere else in the world. The testing was and is too narrow, specific and biased; only looking for specific alleles. The mutations “anywhere within or near the relevant gene” are either ignored or overlooked or not even looked for to begin with. That is why so many people got/get a letter saying they do not have a "known" genetic mutation for Periodic Paralysis. This is definite “bias” in the testing. One is left to believe there is no reason for their symptoms and to wonder about their own sanity. An individual’s doctors, not understanding the above information, believe that the person does not have Periodic Paralysis.

But in reality, I was lucky enough to have a chance to see all of my mutations. Some of my mutations were on different, but recognized exons known to cause PP but were not looked at in the German study. They were not even looked for and some were seen but because they were not the exact allele but right next to it, they were ignored and dismissed. No mention of them was included in the testing result letter. A better way to handle it would have been, first to look at ALL of the known mutations/alleles and then in the letter sent with the results, it should have been stated that similar to my sample letter:

"The results to your DNA testing for Periodic Paralysis are as follows. You have the symptoms of Hyperkalemic Periodic Paralysis. We searched for ALL of the KNOWN mutations for ALL forms of Periodic Paralysis. You do not have the exact and known mutations, but you do have mutations on Exon 7 near the ones that cause Hyperkalemic Periodic Paralysis. Therefore it is likely that you (and possibly your family) have a new or original or unique mutation for Hyperkalemic Periodic Paralysis. This will be documented for your family and for others that may have the same mutation. We need to notify your doctors so that you will be treated from this point on as probably having a form Hyperkalemic Periodic Paralysis. You also need to notify your family members and share this letter with them."

Because this has not happened and I do not expect it to see it happening anytime in the near future and because genetic testing is no longer being done in Germany, and all other testing besides whole genome testing is extremely narrow, diagnosing for Periodic Paralysis must be done by doctors based on the symptoms and characteristics of the individual. This should be done once testing for any other condition in which periods of paralysis or muscle weakness have been ruled out.

The article posted:

http://www.ncbi.nlm.nih.gov/books/NBK7586/?report=reader

 

Until later...