rs878853177

Positions:

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP2PP3_ModeratePP5

The NM_001378452.1(ITPR1):​c.6326A>G​(p.Glu2109Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E2109Q) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 31)

Consequence

ITPR1
NM_001378452.1 missense

Scores

17
1
1

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 9.24
Variant links:
Genes affected
ITPR1 (HGNC:6180): (inositol 1,4,5-trisphosphate receptor type 1) This gene encodes an intracellular receptor for inositol 1,4,5-trisphosphate. Upon stimulation by inositol 1,4,5-trisphosphate, this receptor mediates calcium release from the endoplasmic reticulum. Mutations in this gene cause spinocerebellar ataxia type 15, a disease associated with an heterogeneous group of cerebellar disorders. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), ITPR1. . Gene score misZ 5.5951 (greater than the threshold 3.09). Trascript score misZ 6.2026 (greater than threshold 3.09). GenCC has associacion of gene with spinocerebellar ataxia type 15/16, aniridia-cerebellar ataxia-intellectual disability syndrome, spinocerebellar ataxia type 29.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.909
PP5
Variant 3-4779584-A-G is Pathogenic according to our data. Variant chr3-4779584-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 235921.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr3-4779584-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITPR1NM_001378452.1 linkuse as main transcriptc.6326A>G p.Glu2109Gly missense_variant 49/62 ENST00000649015.2 NP_001365381.1
ITPR1NM_001168272.2 linkuse as main transcriptc.6281A>G p.Glu2094Gly missense_variant 48/61 NP_001161744.1
ITPR1NM_001099952.4 linkuse as main transcriptc.6182A>G p.Glu2061Gly missense_variant 46/59 NP_001093422.2
ITPR1NM_002222.7 linkuse as main transcriptc.6137A>G p.Glu2046Gly missense_variant 45/58 NP_002213.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITPR1ENST00000649015.2 linkuse as main transcriptc.6326A>G p.Glu2109Gly missense_variant 49/62 NM_001378452.1 ENSP00000497605 Q14643-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
31

ClinVar

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

Submissions by phenotype

Gillespie syndrome Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMOct 18, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.56
D
BayesDel_noAF
Pathogenic
0.57
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.96
.;.;.;.;.;.;D;.;.;.
Eigen
Pathogenic
0.92
Eigen_PC
Pathogenic
0.85
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
1.0
D;D;D;D;D;D;D;D;.;D
M_CAP
Pathogenic
0.87
D
MetaRNN
Pathogenic
0.91
D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
3.1
.;.;.;.;.;.;M;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D
PrimateAI
Pathogenic
0.84
D
PROVEAN
Pathogenic
-6.8
D;D;.;D;.;.;.;.;D;.
REVEL
Pathogenic
0.93
Sift
Pathogenic
0.0
D;D;.;D;.;.;.;.;D;.
Sift4G
Pathogenic
0.0
D;D;.;D;.;.;.;.;D;.
Polyphen
1.0
.;.;.;.;.;.;D;.;.;.
Vest4
0.93
MutPred
0.42
.;.;.;.;.;.;Loss of catalytic residue at E2109 (P = 0.0395);.;.;.;
MVP
0.99
MPC
2.1
ClinPred
1.0
D
GERP RS
5.3
Varity_R
0.85
gMVP
0.97

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs878853177; hg19: chr3-4821268; API