rs17847227

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001379150.1(IRS4):​c.3472G>T​(p.Ala1158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000948 in 1,054,944 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 9.5e-7 ( 0 hom. 0 hem. )

Consequence

IRS4
NM_001379150.1 missense

Scores

1
5
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.657
Variant links:
Genes affected
IRS4 (HGNC:6128): (insulin receptor substrate 4) IRS4 encodes the insulin receptor substrate 4, a cytoplasmic protein that contains many potential tyrosine and serine/threonine phosphorylation sites. Tyrosine-phosphorylated IRS4 protein has been shown to associate with cytoplasmic signalling molecules that contain SH2 domains. The IRS4 protein is phosphorylated by the insulin receptor tyrosine kinase upon receptor stimulation.. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.32822698).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRS4NM_001379150.1 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 2 ENST00000372129.4 NP_001366079.1
IRS4NM_003604.2 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 1 NP_003595.1 O14654
IRS4XM_011531061.2 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 3 XP_011529363.1
IRS4XM_006724713.4 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 2 XP_006724776.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IRS4ENST00000372129.4 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 2 6 NM_001379150.1 ENSP00000361202.3 A0A804CF45
IRS4ENST00000564206.2 linkc.3472G>T p.Ala1158Ser missense_variant Exon 1 of 1 6 ENSP00000505547.1 O14654

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
9.48e-7
AC:
1
AN:
1054944
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
339238
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0000599
Gnomad4 EAS exome
AF:
0.00
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.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.61
CADD
Benign
21
DANN
Uncertain
1.0
DEOGEN2
Benign
0.37
T
FATHMM_MKL
Uncertain
0.76
D
LIST_S2
Benign
0.54
T
M_CAP
Pathogenic
0.55
D
MetaRNN
Benign
0.33
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
L
PrimateAI
Uncertain
0.64
T
PROVEAN
Benign
-0.63
N
REVEL
Benign
0.087
Sift
Uncertain
0.0070
D
Sift4G
Uncertain
0.049
D
Polyphen
0.95
P
Vest4
0.22
MutPred
0.23
Gain of glycosylation at A1158 (P = 0.0335);
MVP
0.30
MPC
0.45
ClinPred
0.74
D
GERP RS
3.8
Varity_R
0.14
gMVP
0.11

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-107976103; API