3-4665189-C-T

Variant names:

• chr3-4665189-C-T
• rs1553681680
• NM_001378452.1:c.1606C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001378452.1(ITPR1):​c.1606C>T​(p.Leu536Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,664 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: ITPR1 NM_001378452.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.912
• Publications: 0 publications found

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]

ITPR1 Gene-Disease associations (from GenCC):

• aniridia-cerebellar ataxia-intellectual disability syndrome

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Genomics England PanelApp, PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• spinocerebellar ataxia type 29

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet
• spinocerebellar ataxia type 15/16

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 3-4665189-C-T is Benign according to our data. Variant chr3-4665189-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 503528.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 62	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.1561C>T	p.Leu521Phe	missense_variant	Exon 16 of 61		NP_001161744.1
ITPR1	NM_001099952.4	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 59		NP_001093422.2
ITPR1	NM_002222.7	c.1561C>T	p.Leu521Phe	missense_variant	Exon 16 of 58		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 62		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 62	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 62			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.1561C>T	p.Leu521Phe	missense_variant	Exon 16 of 61			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.1561C>T	p.Leu521Phe	missense_variant	Exon 16 of 61	1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.1561C>T	p.Leu521Phe	missense_variant	Exon 14 of 59			ENSP00000497026.1
ITPR1	ENST00000357086.10	c.1606C>T	p.Leu536Phe	missense_variant	Exon 17 of 59	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.1561C>T	p.Leu521Phe	missense_variant	Exon 16 of 58	1		ENSP00000397885.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461664 Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2 AN XY: 727120

African (AFR) AF: 0.00 AC: 0 AN: 33480

American (AMR) AF: 0.00 AC: 0 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00 AC: 0 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53402

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000180 AC: 2 AN: 1111826

Other (OTH) AF: 0.00 AC: 0 AN: 60372

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Spinocerebellar ataxia type 29 Benign:1

Feb 09, 2018

Schule lab, Hertie Institute for Clinical Brain Research

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Uncertain	0.10	D
BayesDel_noAF	Benign	-0.090
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.92	.;.;.;.;.;.;D;.;.
Eigen	Uncertain	0.44
Eigen_PC	Uncertain	0.38
FATHMM_MKL	Uncertain	0.84	D
LIST_S2	Uncertain	0.90	D;D;D;D;D;D;D;D;.
M_CAP	Uncertain	0.24	D
MetaRNN	Uncertain	0.64	D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.54	D
MutationAssessor	Benign	1.7	L;.;.;.;.;.;L;.;.
PhyloP100		0.91
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-3.5	D;D;D;D;.;.;.;.;D
REVEL	Pathogenic	0.70
Sift	Uncertain	0.010	D;T;T;D;.;.;.;.;T
Sift4G	Uncertain	0.013	D;D;.;D;.;.;.;.;D
Polyphen		0.93	.;.;.;.;.;.;P;.;.
Vest4		0.66
MutPred		0.62		Loss of stability (P = 0.1386);.;Loss of stability (P = 0.1386);.;Loss of stability (P = 0.1386);.;Loss of stability (P = 0.1386);.;.;
MVP		0.73
MPC		1.8
ClinPred		0.97	D
GERP RS		4.6
Varity_R		0.28
gMVP		0.46
Mutation Taster		=29/71	disease causing

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

Other links and lift over

dbSNP: rs1553681680; hg19: chr3-4706873; COSMIC: COSV56992784;