rs774815041

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001008949.3(ITPRIPL1):​c.487C>A​(p.Pro163Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P163S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

ITPRIPL1
NM_001008949.3 missense

Scores

3
7
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.51
Variant links:
Genes affected
ITPRIPL1 (HGNC:29371): (ITPRIP like 1) Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITPRIPL1NM_001008949.3 linkc.487C>A p.Pro163Thr missense_variant Exon 3 of 3 ENST00000439118.3 NP_001008949.1 Q6GPH6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITPRIPL1ENST00000439118.3 linkc.487C>A p.Pro163Thr missense_variant Exon 3 of 3 1 NM_001008949.3 ENSP00000389308.2 Q6GPH6-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Benign
-0.050
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.14
.;.;T;.
Eigen
Uncertain
0.55
Eigen_PC
Uncertain
0.56
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.81
T;T;T;T
M_CAP
Benign
0.014
T
MetaRNN
Uncertain
0.71
D;D;D;D
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.5
.;.;M;.
PrimateAI
Benign
0.40
T
PROVEAN
Pathogenic
-5.4
D;D;D;D
REVEL
Benign
0.26
Sift
Uncertain
0.011
D;D;D;D
Sift4G
Pathogenic
0.0
D;D;D;D
Polyphen
1.0, 1.0
.;.;D;D
Vest4
0.47, 0.48, 0.35
MutPred
0.67
.;.;Loss of glycosylation at T160 (P = 0.0677);.;
MVP
0.54
MPC
0.68
ClinPred
0.99
D
GERP RS
4.9
Varity_R
0.23
gMVP
0.57

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: chr2-96992856; API