rs397514511

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5

The ENST00000298229.7(INPPL1):​c.1201C>T​(p.Arg401Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

INPPL1
ENST00000298229.7 missense

Scores

12
6
1

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 1.92
Variant links:
Genes affected
INPPL1 (HGNC:6080): (inositol polyphosphate phosphatase like 1) The protein encoded by this gene is an SH2-containing 5'-inositol phosphatase that is involved in the regulation of insulin function. The encoded protein also plays a role in the regulation of epidermal growth factor receptor turnover and actin remodelling. Additionally, this gene supports metastatic growth in breast cancer and is a valuable biomarker for breast cancer. [provided by RefSeq, Jan 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.85
PP5
Variant 11-72230799-C-T is Pathogenic according to our data. Variant chr11-72230799-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 39479.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
INPPL1NM_001567.4 linkuse as main transcriptc.1201C>T p.Arg401Trp missense_variant 11/28 ENST00000298229.7 NP_001558.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
INPPL1ENST00000298229.7 linkuse as main transcriptc.1201C>T p.Arg401Trp missense_variant 11/281 NM_001567.4 ENSP00000298229 P1O15357-1
INPPL1ENST00000538751.5 linkuse as main transcriptc.475C>T p.Arg159Trp missense_variant 10/271 ENSP00000444619 O15357-2
INPPL1ENST00000538339.1 linkuse as main transcriptn.82C>T non_coding_transcript_exon_variant 1/22

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000616
AC:
9
AN:
1461370
Hom.:
0
Cov.:
33
AF XY:
0.00000688
AC XY:
5
AN XY:
727016
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000810
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000882
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Opsismodysplasia Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJan 10, 2013- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.50
D
BayesDel_noAF
Pathogenic
0.49
CADD
Pathogenic
30
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.95
D;.;T
Eigen
Uncertain
0.59
Eigen_PC
Uncertain
0.58
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Pathogenic
0.99
D;D;D
M_CAP
Uncertain
0.25
D
MetaRNN
Pathogenic
0.85
D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Uncertain
2.5
M;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Pathogenic
0.93
D
PROVEAN
Pathogenic
-6.9
D;D;.
REVEL
Pathogenic
0.80
Sift
Uncertain
0.0010
D;D;.
Sift4G
Pathogenic
0.0010
D;D;D
Polyphen
1.0
D;.;.
Vest4
0.88
MutPred
0.59
Loss of disorder (P = 0.0109);.;.;
MVP
0.75
MPC
1.7
ClinPred
0.99
D
GERP RS
4.6
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.6
Varity_R
0.65
gMVP
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs397514511; hg19: chr11-71941843; COSMIC: COSV99995920; COSMIC: COSV99995920; API