rs878853177

Variant names:

• chr3-4779584-A-G
• rs878853177
• NM_001378452.1:c.6326A>G

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2 PM5 PP2 PP3_Moderate PP5

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
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.24

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]

ACMG classification

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 the ITPR1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 44 curated pathogenic missense variants (we use a threshold of 10). The gene has 31 curated benign missense variants. Gene score misZ: 5.5951 (above the threshold of 3.09). Trascript score misZ: 6.2026 (above the threshold of 3.09). GenCC associations: The gene is linked to 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 rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.6326A>G	p.Glu2109Gly	missense_variant	Exon 49 of 62	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.6281A>G	p.Glu2094Gly	missense_variant	Exon 48 of 61		NP_001161744.1
ITPR1	NM_001099952.4	c.6182A>G	p.Glu2061Gly	missense_variant	Exon 46 of 59		NP_001093422.2
ITPR1	NM_002222.7	c.6137A>G	p.Glu2046Gly	missense_variant	Exon 45 of 58		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.6326A>G	p.Glu2109Gly	missense_variant	Exon 49 of 62		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.6302A>G	p.Glu2101Gly	missense_variant	Exon 49 of 62	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.6299A>G	p.Glu2100Gly	missense_variant	Exon 49 of 62			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.6284A>G	p.Glu2095Gly	missense_variant	Exon 48 of 61			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.6281A>G	p.Glu2094Gly	missense_variant	Exon 48 of 61	1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.6254A>G	p.Glu2085Gly	missense_variant	Exon 46 of 59			ENSP00000497026.1
ITPR1	ENST00000357086.10	c.6182A>G	p.Glu2061Gly	missense_variant	Exon 46 of 59	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.6137A>G	p.Glu2046Gly	missense_variant	Exon 45 of 58	1		ENSP00000397885.2
ITPR1	ENST00000648038.1	c.4088A>G	p.Glu1363Gly	missense_variant	Exon 29 of 42			ENSP00000497872.1
ITPR1	ENST00000648431.1	c.3626A>G	p.Glu1209Gly	missense_variant	Exon 27 of 39			ENSP00000498149.1
ITPR1	ENST00000648212.1	c.3233A>G	p.Glu1078Gly	missense_variant	Exon 25 of 39			ENSP00000498022.1

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

Submissions by phenotype

Gillespie syndrome Pathogenic:1

Oct 18, 2017

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;.;.;.
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

Other links and lift over

dbSNP: rs878853177; hg19: chr3-4821268;