rs3749383

Variant names:

• chr3-4697153-A-G
• rs3749383
• NM_001378452.1:c.4288A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001378452.1(ITPR1):​c.4288A>G​(p.Ile1430Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,610,434 control chromosomes in the GnomAD database, including 50 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0014 (6 hom., cov: 31)
  • Exomes 𝑓: 0.0012 (44 hom.)
• Consequence: ITPR1 NM_001378452.1 missense
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 7.42
• Publications: 6 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: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0076238215).
• BP6: Variant 3-4697153-A-G is Benign according to our data. Variant chr3-4697153-A-G is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 345737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00137 (209/152300) while in subpopulation EAS AF = 0.0359 (186/5176). AF 95% confidence interval is 0.0317. There are 6 homozygotes in GnomAd4. There are 119 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.4288A>G	p.Ile1430Val	missense_variant	Exon 34 of 62	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.4243A>G	p.Ile1415Val	missense_variant	Exon 33 of 61		NP_001161744.1
ITPR1	NM_001099952.4	c.4261A>G	p.Ile1421Val	missense_variant	Exon 34 of 59		NP_001093422.2
ITPR1	NM_002222.7	c.4216A>G	p.Ile1406Val	missense_variant	Exon 33 of 58		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.4288A>G	p.Ile1430Val	missense_variant	Exon 34 of 62		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.4261A>G	p.Ile1421Val	missense_variant	Exon 34 of 62	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.4261A>G	p.Ile1421Val	missense_variant	Exon 34 of 62			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.4243A>G	p.Ile1415Val	missense_variant	Exon 33 of 61			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.4243A>G	p.Ile1415Val	missense_variant	Exon 33 of 61	1		ENSP00000401671.2
ITPR1	ENST00000648309.1	c.4216A>G	p.Ile1406Val	missense_variant	Exon 31 of 59			ENSP00000497026.1
ITPR1	ENST00000357086.10	c.4261A>G	p.Ile1421Val	missense_variant	Exon 34 of 59	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.4216A>G	p.Ile1406Val	missense_variant	Exon 33 of 58	1		ENSP00000397885.2
ITPR1	ENST00000648038.1	c.2098A>G	p.Ile700Val	missense_variant	Exon 15 of 42			ENSP00000497872.1
ITPR1	ENST00000648431.1	c.1588A>G	p.Ile530Val	missense_variant	Exon 12 of 39			ENSP00000498149.1
ITPR1	ENST00000648212.1	c.1195A>G	p.Ile399Val	missense_variant	Exon 10 of 39			ENSP00000498022.1

Frequencies

GnomAD3 genomes AF: 0.00137 AC: 209 AN: 152182 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0359

Gnomad SAS AF: 0.00165

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00287 AC: 699 AN: 243204 AF XY: 0.00276

Gnomad AFR exome AF: 0.000336

Gnomad AMR exome AF: 0.000148

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0377

Gnomad FIN exome AF: 0.000140

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00134

GnomAD4 exome AF: 0.00119 AC: 1741 AN: 1458134 Hom.: 44 Cov.: 32 AF XY: 0.00116 AC XY: 844 AN XY: 724910

African (AFR) AF: 0.000209 AC: 7 AN: 33438

American (AMR) AF: 0.000113 AC: 5 AN: 44240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26012

East Asian (EAS) AF: 0.0368 AC: 1458 AN: 39660

South Asian (SAS) AF: 0.000820 AC: 70 AN: 85370

European-Finnish (FIN) AF: 0.000169 AC: 9 AN: 53290

Middle Eastern (MID) AF: 0.000173 AC: 1 AN: 5764

European-Non Finnish (NFE) AF: 0.0000225 AC: 25 AN: 1110078

Other (OTH) AF: 0.00275 AC: 166 AN: 60282

GnomAD4 genome AF: 0.00137 AC: 209 AN: 152300 Hom.: 6 Cov.: 31 AF XY: 0.00160 AC XY: 119 AN XY: 74474

African (AFR) AF: 0.0000963 AC: 4 AN: 41558

American (AMR) AF: 0.000131 AC: 2 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.0359 AC: 186 AN: 5176

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4830

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10618

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000147 AC: 1 AN: 68036

Other (OTH) AF: 0.00284 AC: 6 AN: 2112

Alfa AF: 0.00128 Hom.: 7

Bravo AF: 0.00161

ESP6500AA AF: 0.000531 AC: 2

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.00291 AC: 351

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jan 11, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 22, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Benign:1

Oct 15, 2020

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Gillespie syndrome;C1847725:Spinocerebellar ataxia type 15/16;C1861732:Spinocerebellar ataxia type 29 Benign:1

Aug 23, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal dominant cerebellar ataxia Benign:1

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.37	.;.;.;.;.;.;T;.;.;.
Eigen	Benign	0.0011
Eigen_PC	Benign	0.18
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.88	D;D;D;D;D;D;D;D;.;D
MetaRNN	Benign	0.0076	T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	0.69	.;.;.;.;.;.;N;.;.;.
PhyloP100		7.4
PrimateAI	Uncertain	0.75	T
PROVEAN	Benign	0.15	N;N;.;N;.;.;.;.;N;.
REVEL	Benign	0.14
Sift	Benign	0.30	T;T;.;T;.;.;.;.;T;.
Sift4G	Benign	0.28	T;T;.;T;.;.;.;.;T;.
Polyphen		0.059	.;.;.;.;.;.;B;.;.;.
Vest4		0.28
MVP		0.21
MPC		0.64
ClinPred		0.033	T
GERP RS		5.1
Varity_R		0.097
gMVP		0.13
Mutation Taster		=79/21	polymorphism

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: rs3749383; hg19: chr3-4738837;