PYHIN1

pyrin and HIN domain family member 1, the group of Pyrin and HIN domain family|Pyrin domain containing

Basic information

Region (hg38): 1:158930795-158977059

Links

ENSG00000163564 ∙ NCBI:149628 ∙ OMIM:612677 ∙ HGNC:28894 ∙ Uniprot:Q6K0P9 ∙ 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 PYHIN1 gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PYHIN1 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in PYHIN1

This is a list of pathogenic ClinVar variants found in the PYHIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158937019-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-158938480-C-T		not specified	Uncertain significance (Feb 13, 2024)
1-158938501-C-G		not specified	Uncertain significance (Sep 26, 2023)
1-158939091-A-C		not specified	Uncertain significance (Dec 28, 2023)
1-158939174-C-T		not specified	Likely benign (Apr 28, 2022)
1-158939189-G-A		not specified	Uncertain significance (Aug 13, 2021)
1-158939192-G-T		not specified	Uncertain significance (Oct 13, 2021)
1-158939215-T-C		not specified	Uncertain significance (Sep 15, 2021)
1-158941978-G-A		not specified	Likely benign (Jan 27, 2022)
1-158941999-G-A		Malignant tumor of prostate	Uncertain significance (-)
1-158942029-G-A		not specified	Uncertain significance (Jun 23, 2021)
1-158942046-G-A		not specified	Uncertain significance (Mar 30, 2022)
1-158942125-T-C		not specified	Uncertain significance (Jun 16, 2023)
1-158942196-A-G		not specified	Uncertain significance (Mar 24, 2023)
1-158942198-A-T		not specified	Uncertain significance (Jul 06, 2021)
1-158942227-G-A		not specified	Likely benign (Sep 26, 2023)
1-158942338-T-A		not specified	Uncertain significance (Dec 07, 2021)
1-158942388-A-T		PYHIN1-related disorder	Uncertain significance (Feb 03, 2024)
1-158942390-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-158943910-T-C		not specified	Uncertain significance (Mar 20, 2023)
1-158943941-T-C		not specified	Uncertain significance (Sep 22, 2022)
1-158943961-A-G		not specified	Uncertain significance (Jun 13, 2023)
1-158944942-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-158944943-G-T		not specified	Uncertain significance (Apr 07, 2022)
1-158945010-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PYHIN1	protein_coding	protein_coding	ENST00000368140	7	46259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.78e-10	0.268	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.135	270	264	1.02	0.0000137	3220
Missense in Polyphen		64	66.255	0.96596		917
Synonymous	1.28	77	92.7	0.831	0.00000481	954
Loss of Function	0.742	16	19.5	0.819	0.00000104	271

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000670	0.0000670
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Major mediator of the tumor suppressor activity of IFN in breast cancer cells. Promotes ubiquitination and subsequent degradation of MDM2, which leads to p53/TP53 stabilization. Promotes ubiquitination and subsequent degradation of HDAC1, which in turn enhances maspin expression, and impairs invasive activity of cancer cells. {ECO:0000269|PubMed:16479015, ECO:0000269|PubMed:18247378}.

Recessive Scores

• pRec: 0.0614

Intolerance Scores

• loftool: 0.989
• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.0365
• hipred: N
• hipred_score: 0.132
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.705

Gene Damage Prediction

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

Gene ontology

• Biological process: activation of innate immune response;cell cycle;protein destabilization;cellular response to interferon-alpha;cellular response to interferon-beta;positive regulation of DNA binding;positive regulation of transcription, DNA-templated;protein stabilization;positive regulation of protein localization to nucleus;positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;positive regulation of ubiquitin-dependent protein catabolic process
• Cellular component: nuclear speck;protein-containing complex
• Molecular function: ubiquitin protein ligase binding