ITPRID1

ITPR interacting domain containing 1

Basic information

Region (hg38): 7:31514089-31656504

Previous symbols: [ "CCDC129" ]

Links

ENSG00000180347 ∙ NCBI:223075 ∙ ∙ HGNC:27363 ∙ Uniprot:Q6ZRS4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ITPRID1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITPRID1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			52	6		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	6	0

Variants in ITPRID1

This is a list of pathogenic ClinVar variants found in the ITPRID1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-31553112-G-A		not specified	Uncertain significance (Jan 24, 2024)
7-31553113-C-T		not specified	Uncertain significance (Dec 06, 2021)
7-31553124-C-A		not specified	Uncertain significance (Oct 25, 2022)
7-31553142-C-G		not specified	Uncertain significance (Oct 06, 2021)
7-31554484-A-C		not specified	Uncertain significance (Jul 27, 2023)
7-31554872-A-C		not specified	Uncertain significance (Nov 17, 2022)
7-31554895-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-31569776-G-A		not specified	Uncertain significance (Nov 05, 2021)
7-31572107-T-C		not specified	Uncertain significance (Aug 08, 2023)
7-31572148-A-C		not specified	Uncertain significance (Dec 21, 2023)
7-31572169-A-G		not specified	Likely benign (Apr 22, 2024)
7-31574563-G-A			Uncertain significance (-)
7-31574581-A-G		not specified	Uncertain significance (Jun 29, 2023)
7-31574637-C-T		not specified	Uncertain significance (Dec 15, 2022)
7-31574646-T-C		not specified	Uncertain significance (Aug 01, 2022)
7-31574686-G-T		not specified	Uncertain significance (May 30, 2024)
7-31577922-A-G		not specified	Uncertain significance (Aug 12, 2021)
7-31577950-C-G		not specified	Uncertain significance (May 17, 2023)
7-31577976-G-A		not specified	Uncertain significance (Mar 07, 2024)
7-31578000-G-A		not specified	Likely benign (Dec 21, 2023)
7-31578049-A-G		not specified	Uncertain significance (Dec 18, 2023)
7-31578055-A-G		not specified	Likely benign (Feb 17, 2024)
7-31578066-G-A		not specified	Uncertain significance (Jan 10, 2022)
7-31578087-G-A		not specified	Uncertain significance (Nov 21, 2023)
7-31578105-G-A		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITPRID1	protein_coding	protein_coding	ENST00000451887	15	144631

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.55e-36	0.00000121	125396	2	189	125587	0.000761

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.354	563	540	1.04	0.0000263	6926
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00260	0.00253
Ashkenazi Jewish	0.000111	0.0000993
East Asian	0.000441	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000373	0.000361
Middle Eastern	0.000441	0.000435
South Asian	0.00306	0.00285
Other	0.000997	0.000979

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.83
• rvis_percentile_EVS: 97.04

Haploinsufficiency Scores

• pHI: 0.0548
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Itprid1

Gene ontology

• Molecular function: signaling receptor binding