chr2-98520695-C-T
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001134225.2(INPP4A):c.115C>T(p.Gln39Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000149 in 1,343,344 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). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000015 ( 0 hom. )
Consequence
INPP4A
NM_001134225.2 stop_gained
NM_001134225.2 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 5.04
Genes affected
INPP4A (HGNC:6074): (inositol polyphosphate-4-phosphatase type I A) This gene encodes an Mg++ independent enzyme that hydrolyzes the 4-position phosphate from the inositol ring of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4-trisphosphate, and inositol 3,4-bisphosphate. Multiple transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 2-98520695-C-T is Pathogenic according to our data. Variant chr2-98520695-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 801338.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-98520695-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INPP4A | NM_001134225.2 | c.115C>T | p.Gln39Ter | stop_gained | 4/25 | ENST00000409851.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INPP4A | ENST00000409851.8 | c.115C>T | p.Gln39Ter | stop_gained | 4/25 | 1 | NM_001134225.2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000149 AC: 2AN: 1343344Hom.: 0 Cov.: 24 AF XY: 0.00000150 AC XY: 1AN XY: 665530
GnomAD4 exome
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2
AN:
1343344
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Cov.:
24
AF XY:
AC XY:
1
AN XY:
665530
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Intellectual disability Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Department of Medical Genetics, Ahvaz Jundishapur University of Medical Sciences | Dec 01, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;A;A;A;A
Vest4
GERP RS
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