GET-Evidence: Search

VariantImpactInheritance patternSummaryGenomes
SCN9A R26Hinsufficiently evaluated not reviewed, f=0.000unknown
SCN9A I62Vlikely pathogenicdominant

Reported by ClinVar to cause familial febrile seizures ( In ClinVar this variant is reported as “pathogenic” by OMIM. However, it is classified as “uncertain significance” by GeneDx. OMIM’s submission refers to Singh et al 2009 (, where this variant was observed in one of 92 patients with childhood febrile seizures.

This patient was Hispanic/Latino; according to ExAC data, this variant is rare in all ancestries tested (less than 1 in 1,000 carry it) including Latino ( The statistical significance of Singh et al’s observation is unclear, and may weak or absent.

(4 web hits)

SCN9A F98Linsufficiently evaluated not reviewed, f=0.008unknown var-GS19017-1100-36-ASM
SCN9A P149Qinsufficiently evaluated pathogenicunknown

(4 web hits)

SCN9A R185Hinsufficiently evaluated none, f=0.006unknown
SCN9A F216Sinsufficiently evaluated pathogenicunknown

(33 web hits)

SCN9A I228Minsufficiently evaluated none, f=0.001unknown
SCN9A S241Tinsufficiently evaluated pathogenicunknown

(80 web hits)

SCN9A R277Xinsufficiently evaluated pathogenicunknown

(2 web hits)

SCN9A Y328Xinsufficiently evaluated pathogenicunknown

(3 web hits)

SCN9A T370Minsufficiently evaluated not reviewed, f=0.001unknown var-GS21767-1100-36-ASM
SCN9A S459Xinsufficiently evaluated pathogenicunknown

(49 web hits)

SCN9A S490Ninsufficiently evaluated none, f=0.042unknown

(1 web hit)

SCN9A P610Tinsufficiently evaluated not reviewed, f=0.020unknown

(13 web hits)

CGI sample GS01173-DNA_C02 from PGP sample 10366372
hu34D5B9 exome
CGI sample GS01669-DNA_B03 from PGP sample 14427241
hu728FFF build 36 substitution variants
SCN9A N641Yinsufficiently evaluated pathogenicunknown

(24 web hits)

SCN9A K655Runcertain benign, f=0.001unknown

Singh et al. 2009 studied a large family with febrile seizures, linking this region as causal. Then, analyzing a panel of 92 patients with childhood febrile seizures, and 109 Dravet cases (total of 201 patients), they saw 3 carriers of this variant (once in former, twice in latter), and not it in 562 Caucasian control chromosomes (281 individuals). Neither patient nor control findings have a statistically significant difference the variant frequency according to ExAC data (where 1 in 173 are carriers). This paper was proposing a high penetrance hypothesis, but if this were true we would see a dramatic enrichment of the variant in patients.

(3 web hits)

SCN9A W719Cinsufficiently evaluated not reviewed, f=0.004unknown var-GS19129-1100-36-ASM
SCN9A I720Klikely pathogenicdominant

This variant is reported to cause erythromelalgia (burning pain, warmth, and redness of the extremities) and/or small fiber neuropathy in a dominant fashion. These reports are recorded in ClinVar by Baylor Miraca Genetics Lab and OMIM, respectively ( However, ExAC data suggests 1 in 2,000 of European ancestry carry this variant, far exceeding the prevalence of the trait (erythromelalgia affects about 1 in 100,000). ExAC also notes variant data here may be low quality (which could affect their own database and genome data from other sources).

SCN9A I848Tinsufficiently evaluated pathogenicunknown

(66 web hits)

SCN9A L858Finsufficiently evaluated pathogenicunknown

(69 web hits)

SCN9A L858Hinsufficiently evaluated pathogenicunknown

(54 web hits)

SCN9A W897Xinsufficiently evaluated pathogenicunknown

(45 web hits)

SCN9A V991Linsufficiently evaluated not reviewed, f=0.004unknown var-GS19670-1100-36-ASM
SCN9A R996Cinsufficiently evaluated pathogenicunknown

(15 web hits)

SCN9A K1006Ninsufficiently evaluated not reviewed, f=0.001unknown var-GS19020-1100-36-ASM
SCN9A S1099Linsufficiently evaluated not reviewed, f=0.001unknown var-GS19701-1100-36-ASM
SCN9A R1110Qinsufficiently evaluated not reviewed, f=0.024unknown var-GS12004-1100-36-ASM
CGI sample GS01173-DNA_A07 from PGP sample 96240009
SCN9A W1150Rinsufficiently evaluated benign, f=0.878dominant

The Trp variant was initially reported causative in a sporadic case of primary erythermalgia, but it was later determined to be a benign polymorphism.

(17 web hits)

CGI sample GS00253-DNA_E01_200_37
CGI sample GS01669-DNA_C07 from PGP sample 74521372 (hom)
CGI sample GS01173-DNA_C02 from PGP sample 10366372 (hom)
CGI sample GS01175-DNA_G03 from PGP sample 92527586 (hom)
var-GS19025-1100-36-ASM (hom)
CGI sample GS01669-DNA_F02 from PGP sample 40767107 (hom)
CGI sample GS01175-DNA_H01 from PGP sample 94797469 (hom)
hu34D5B9 exome (hom)
hu3215A7 build 36 substitution variants (hom)
PGP13 (hu3A8D13) build 37, from CGI var (software ver
var-GS18942-1100-36-ASM (hom)
CGI sample GS01669-DNA_C05 from PGP sample 42408046 (hom)
var-GS19020-1100-36-ASM (hom)
CGI sample GS01173-DNA_F02 from PGP sample 70008981 (hom)
var-GS19700-1100-36-ASM (hom)
var-GS18501-1100-36-ASM (hom)
var-GS18504-1100-36-ASM (hom)
var-GS18558-1100-36-ASM (hom)
var-GS19735-1100-36-ASM (hom)
CGI sample GS01173-DNA_G02 from PGP sample 67180598 (hom)
CGI sample GS000006909
CGI sample GS01175-DNA_B05 from PGP sample 83494370 (hom)
var-GS07357-1100-36-ASM (hom)
CGI sample GS000005532 (hom)
var-GS19703-1100-36-ASM (hom)
hu232307 build 36 substitution variants (hom)
CGI sample GS01173-DNA_H06 from PGP sample 91708424 (hom)
CGI sample GS01669-DNA_B03 from PGP sample 14427241 (hom)
CGI sample GS00253-DNA_G01_200_37 (hom)
CGI sample GS01175-DNA_A04 from PGP sample 13272228 (hom)
var-GS19704-1100-36-ASM (hom)
var-GS10851-1100-36-ASM (hom)
CGI sample GS00253-DNA_A01_200_37 (hom)
CGI sample GS01173-DNA_D06 from PGP sample 69488604 (hom)
var-GS19239-1100-36-ASM (hom)
var-GS19017-1100-36-ASM (hom)
var-GS18502-1100-36-ASM (hom)
var-GS19649-1100-36-ASM (hom)
var-GS18555-1100-36-ASM (hom)
CGI sample GS01669-DNA_B05 from PGP sample 86486261 (hom)
var-GS19648-1100-36-ASM (hom)
var-GS18537-1100-36-ASM (hom)
CGI sample GS01669-DNA_D02 from PGP sample 27316983
CGI sample GS00253-DNA_B02_200_37 (hom)
CGI sample GS01669-DNA_H05 from PGP sample 10971581 (hom)
CGI sample GS00253-DNA_B01_200_37 (hom)
CGI sample GS01173-DNA_F06 from PGP sample 64191565 (hom)
CGI sample GS01175-DNA_D05 from PGP sample 1205491 (hom)
CGI sample GS00253-DNA_F01_200_37 (hom)
var-GS20502-1100-36-ASM (hom)
CGI sample GS01175-DNA_B01 from PGP sample 86206034
CGI sample GS01175-DNA_D01 from PGP sample 31286272
var-GS19129-1100-36-ASM (hom)
CGI sample GS00253-DNA_D01_200_37 (hom)
var-GS19240-1100-36-ASM (hom)
CGI sample GS00253-DNA_C01_200_37 (hom)
hu728FFF build 36 substitution variants
var-GS18947-1100-36-ASM (hom)
var-GS18505-1100-36-ASM (hom)
var-GS19670-1100-36-ASM (hom)
CGI sample GS00253-DNA_A02_200_37
CGI sample GS00253-DNA_H01_200_37 (hom)
CGI sample GS01669-DNA_A04 from PGP sample 08188426 (hom)
CGI sample GS01175-DNA_F02 from PGP sample 95788191 (hom)
CGI sample GS01175-DNA_B04 from PGP sample 88590671
CGI sample GS01173-DNA_B02 from PGP sample 94378523 (hom)
CGI sample GS01173-DNA_A07 from PGP sample 96240009
CGI sample GS01173-DNA_B07 from PGP sample 61499538 (hom)
var-GS18508-1100-36-ASM (hom)
var-GS19026-1100-36-ASM (hom)
var-GS18940-1100-36-ASM (hom)
var-GS06985-1100-36-ASM (hom)
var-GS18517-1100-36-ASM (hom)
CGI sample GS01175-DNA_D03 from PGP sample 27486199 (hom)
SCN9A I1159Tinsufficiently evaluated not reviewed, f=0.001unknown var-GS19239-1100-36-ASM
SCN9A N1245Sinsufficiently evaluated not reviewed, f=0.005unknown CGI sample GS00253-DNA_F01_200_37
SCN9A V1298Dinsufficiently evaluated pathogenicunknown

(16 web hits)

SCN9A V1298Finsufficiently evaluated pathogenicunknown

(14 web hits)

SCN9A V1299Finsufficiently evaluated pathogenicunknown

(13 web hits)

SCN9A V1369Ainsufficiently evaluated not reviewedunknown
SCN9A F1449Vinsufficiently evaluated pathogenicunknown

(71 web hits)

SCN9A I1461Tinsufficiently evaluated pathogenicunknown

(27 web hits)

SCN9A T1464Iinsufficiently evaluated pathogenicunknown

(17 web hits)

SCN9A D1908Ginsufficiently evaluated not reviewed, f=0.005unknown var-GS19735-1100-36-ASM
CGI sample GS01669-DNA_A04 from PGP sample 08188426
SCN9A L1916Finsufficiently evaluated not reviewed, f=0.003unknown
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Total results: 39

Gene search

"GENE" or "GENE A123C":

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