X-108732669-G-T
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001379150.1(IRS4):c.3676C>A(p.Pro1226Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000228 in 1,098,213 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.000023 ( 0 hom. 6 hem. )
Consequence
IRS4
NM_001379150.1 missense
NM_001379150.1 missense
Scores
4
3
10
Clinical Significance
Conservation
PhyloP100: 2.60
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.06737661).
BS2
High Hemizygotes in GnomAdExome4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IRS4 | NM_001379150.1 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/2 | ENST00000372129.4 | NP_001366079.1 | |
IRS4 | NM_003604.2 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/1 | NP_003595.1 | ||
IRS4 | XM_011531061.2 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/3 | XP_011529363.1 | ||
IRS4 | XM_006724713.4 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/2 | XP_006724776.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IRS4 | ENST00000372129.4 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/2 | 6 | NM_001379150.1 | ENSP00000361202.3 | ||
IRS4 | ENST00000564206.2 | c.3676C>A | p.Pro1226Thr | missense_variant | 1/1 | 6 | ENSP00000505547.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
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23
GnomAD3 exomes AF: 0.000136 AC: 25AN: 183499Hom.: 0 AF XY: 0.0000883 AC XY: 6AN XY: 67941
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GnomAD4 exome AF: 0.0000228 AC: 25AN: 1098213Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 6AN XY: 363571
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GnomAD4 genome Cov.: 23
GnomAD4 genome
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23
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.3676C>A (p.P1226T) alteration is located in exon 1 (coding exon 1) of the IRS4 gene. This alteration results from a C to A substitution at nucleotide position 3676, causing the proline (P) at amino acid position 1226 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Pathogenic
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;L
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;N
REVEL
Benign
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
0.61
.;P
Vest4
0.14
MutPred
0.20
.;Gain of phosphorylation at P1226 (P = 0.0019);
MVP
MPC
0.55
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at