HIRIP3

HIRA interacting protein 3

Basic information

Region (hg38): 16:29992330-29996074

Links

ENSG00000149929 ∙ NCBI:8479 ∙ OMIM:603365 ∙ HGNC:4917 ∙ Uniprot:Q9BW71 ∙ 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 HIRIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIRIP3 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			55	2		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	2	0

Variants in HIRIP3

This is a list of pathogenic ClinVar variants found in the HIRIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29993220-C-T		not specified	Uncertain significance (Dec 25, 2024)
16-29993247-T-C		not specified	Uncertain significance (Dec 23, 2024)
16-29993266-C-T		not specified	Uncertain significance (Dec 06, 2022)
16-29993278-G-A		not specified	Uncertain significance (Mar 01, 2023)
16-29993296-G-C		not specified	Uncertain significance (Dec 28, 2023)
16-29993301-C-T		not specified	Uncertain significance (Dec 07, 2023)
16-29993304-C-T		not specified	Uncertain significance (Jul 30, 2024)
16-29993345-C-G		not specified	Uncertain significance (Apr 19, 2023)
16-29993362-G-A		not specified	Uncertain significance (Jul 12, 2022)
16-29993467-C-T		not specified	Uncertain significance (Dec 23, 2024)
16-29993497-A-G		not specified	Uncertain significance (Aug 12, 2022)
16-29993536-C-G		not specified	Uncertain significance (Dec 14, 2022)
16-29993552-G-A		not specified	Uncertain significance (Nov 25, 2024)
16-29993667-C-A		not specified	Uncertain significance (Sep 27, 2022)
16-29993670-G-A		not specified	Uncertain significance (Sep 08, 2024)
16-29993733-G-A		not specified	Uncertain significance (Feb 26, 2024)
16-29993748-G-A		not specified	Uncertain significance (Oct 04, 2022)
16-29993778-G-C		not specified	Uncertain significance (Mar 22, 2023)
16-29993779-G-C		not specified	Uncertain significance (Nov 25, 2024)
16-29993786-T-A		not specified	Uncertain significance (Oct 25, 2023)
16-29993796-G-A		not specified	Uncertain significance (Apr 29, 2024)
16-29993920-C-T		not specified	Uncertain significance (Oct 29, 2024)
16-29993935-C-T		not specified	Uncertain significance (Nov 14, 2023)
16-29993975-G-C		not specified	Uncertain significance (Dec 11, 2023)
16-29994012-G-A		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIRIP3	protein_coding	protein_coding	ENST00000279392	7	4113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000198	0.974	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.821	366	324	1.13	0.0000182	3628
Missense in Polyphen		99	87.373	1.1331		935
Synonymous	-0.933	136	123	1.11	0.00000644	1068
Loss of Function	2.06	13	23.8	0.546	0.00000135	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000373	0.000372
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000218	0.000217
South Asian	0.000490	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in chromatin function and histone metabolism via its interaction with HIRA and histones. {ECO:0000269|PubMed:9710638}.
• Pathway: De novo fatty acid biosynthesis (Consensus)

Recessive Scores

• pRec: 0.0907

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.52

Haploinsufficiency Scores

• pHI: 0.244
• hipred: N
• hipred_score: 0.324
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hirip3

Zebrafish Information Network

• Gene name: hirip3
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: chromatin assembly or disassembly
• Cellular component: nucleus;nucleolus
• Molecular function: protein binding