ITPRID2

ITPR interacting domain containing 2

Basic information

Region (hg38): 2:181891729-181930738

Previous symbols: [ "SSFA2" ]

Links

ENSG00000138434 ∙ NCBI:6744 ∙ OMIM:118990 ∙ HGNC:11319 ∙ Uniprot:P28290 ∙ 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 ITPRID2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITPRID2 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			80	4		84
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	80	4	0

Variants in ITPRID2

This is a list of pathogenic ClinVar variants found in the ITPRID2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-181892124-G-A		not specified	Uncertain significance (Jun 08, 2022)
2-181892128-G-T		not specified	Uncertain significance (Sep 12, 2023)
2-181892131-G-A		not specified	Uncertain significance (Sep 12, 2023)
2-181892229-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-181892240-C-G		not specified	Uncertain significance (Jun 07, 2024)
2-181892262-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-181892271-G-A		not specified	Uncertain significance (Jan 31, 2022)
2-181896065-G-A		not specified	Uncertain significance (Mar 20, 2024)
2-181898883-A-G		not specified	Uncertain significance (Dec 18, 2023)
2-181899019-A-G		not specified	Uncertain significance (May 24, 2024)
2-181899084-T-A		not specified	Uncertain significance (May 13, 2024)
2-181900719-A-G		not specified	Uncertain significance (Jun 10, 2022)
2-181900739-A-G		not specified	Uncertain significance (Jun 16, 2024)
2-181900763-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-181900764-G-A		not specified	Uncertain significance (Feb 11, 2022)
2-181900779-T-C		not specified	Uncertain significance (Mar 29, 2022)
2-181900854-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-181901786-G-C		not specified	Uncertain significance (Jun 29, 2023)
2-181901837-G-A		not specified	Uncertain significance (May 24, 2023)
2-181901859-G-A		not specified	Uncertain significance (May 15, 2023)
2-181901864-A-G		not specified	Uncertain significance (Jul 09, 2021)
2-181901867-T-A		not specified	Uncertain significance (Sep 13, 2023)
2-181901922-A-G		not specified	Uncertain significance (Jul 06, 2022)
2-181901933-C-T		not specified	Uncertain significance (Mar 20, 2024)
2-181902008-C-T		not specified	Uncertain significance (Mar 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITPRID2	protein_coding	protein_coding	ENST00000431877	17	38906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.35e-7	1.00	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.408	697	667	1.04	0.0000339	8207
Missense in Polyphen		279	296.93	0.93963		3741
Synonymous	0.667	229	242	0.945	0.0000122	2460
Loss of Function	4.29	21	55.5	0.378	0.00000283	721

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000335
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000598	0.000598
South Asian	0.000262	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.6

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.443
• ghis: 0.449

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Itprid2
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Cellular component: nucleus;cytosol;plasma membrane
• Molecular function: signaling receptor binding;actin filament binding