rs201569378

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_001365536.1(SCN9A):ā€‹c.1675G>Cā€‹(p.Gly559Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

SCN9A
NM_001365536.1 missense

Scores

3
11
5

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.87
Variant links:
Genes affected
SCN9A (HGNC:10597): (sodium voltage-gated channel alpha subunit 9) This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]
SCN1A-AS1 (HGNC:54069): (SCN1A and SCN9A antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.761

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCN9ANM_001365536.1 linkc.1675G>C p.Gly559Arg missense_variant 12/27 ENST00000642356.2 NP_001352465.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCN9AENST00000642356.2 linkc.1675G>C p.Gly559Arg missense_variant 12/27 NM_001365536.1 ENSP00000495601.1 Q15858-1
SCN9AENST00000303354.11 linkc.1675G>C p.Gly559Arg missense_variant 12/275 ENSP00000304748.7 Q15858-1
SCN9AENST00000409672.5 linkc.1675G>C p.Gly559Arg missense_variant 12/275 ENSP00000386306.1 Q15858-3
SCN9AENST00000645907.1 linkc.1675G>C p.Gly559Arg missense_variant 12/27 ENSP00000495983.1 Q15858-4
SCN9AENST00000454569.6 linkc.1675G>C p.Gly559Arg missense_variant 12/151 ENSP00000413212.2 A0A0C4DG82

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461584
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
727074
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000827
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.21
BayesDel_addAF
Uncertain
0.049
T
BayesDel_noAF
Uncertain
0.0
CADD
Benign
22
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.55
.;D;.;.;D;.;.
Eigen
Benign
-0.038
Eigen_PC
Benign
0.0095
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.92
D;.;D;D;D;D;D
M_CAP
Uncertain
0.12
D
MetaRNN
Pathogenic
0.76
D;D;D;D;D;D;D
MetaSVM
Uncertain
0.58
D
MutationAssessor
Uncertain
2.3
M;M;M;.;M;M;.
PrimateAI
Uncertain
0.61
T
PROVEAN
Pathogenic
-4.7
D;.;.;.;.;D;.
REVEL
Uncertain
0.55
Sift
Uncertain
0.020
D;.;.;.;.;D;.
Sift4G
Benign
0.088
T;T;.;.;.;T;.
Polyphen
0.38
.;B;.;.;B;.;.
Vest4
0.62
MVP
0.79
MPC
0.18
ClinPred
0.84
D
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.38
gMVP
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201569378; hg19: chr2-167141262; API