ITPRID1

protein-coding

ITPR interacting domain containing 1

Gene summary

Predicted to enable signaling receptor binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CCDC129

MANE transcript

NM_001257967.3

Inheritance

—

ClinVar variants

U:151B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.1

Max pathogenic AF

—

Genomic locus

chr7:31,514,090-31,656,504

External References & Databases

Ensembl (ENSG00000180347)

Transcript & Mutation Effects

hg38 • Region Span ~142.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ITPRID1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 155

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001257967.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			146 clinvar	11 clinvar		157
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	151	12	0	163

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001257967.3	RefSeq	NP_001244896.2	13	MANE Select
ENST00000615280.5	Ensembl	ENSP00000478518.2	13	MANE Select
NM_001257968.3	RefSeq	NP_001244897.2	14	Standard
NM_194300.5	RefSeq	NP_919276.2	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

signaling receptor binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451887
Coding exons: 15
Length: 144631
Individuals with no LoFs: 125396
Homozygous LoFs: 2
Heterozygous LoFs: 189
Defined: 125587
p: 0.000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.354	563	540	1.04	0.0000263	6926
Missense (PolyPhen)		143	133.47	1.0714		1950
Synonymous	-0.573	212	202	1.05	0.0000105	2012
Loss of Function	-0.650	51	46.2	1.10	0.00000240	566

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0021	notable
Latino/Admixed American	0.00043	0.00040	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00037	0.00036	rare
South Asian	0.0031	0.0028	notable
Other	0.0010	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.83
RVIS percentile EVS: 97.04

Essentials

Essential (gene trap): N