SINHCAF

SIN3-HDAC complex associated factor

Basic information

Region (hg38): 12:31280584-31327058

Previous symbols: [ "C12orf14", "FAM60A" ]

Links

ENSG00000139146 ∙ NCBI:58516 ∙ OMIM:615027 ∙ HGNC:30702 ∙ Uniprot:Q9NP50 ∙ 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 SINHCAF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SINHCAF 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				1		1
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	4	1	0

Variants in SINHCAF

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

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

Position	Type	Phenotype	Significance	ClinVar
12-31282740-G-A		not specified	Uncertain significance (Nov 21, 2024)
12-31287671-G-A		not specified	Uncertain significance (May 22, 2024)
12-31287730-T-G		not specified	Uncertain significance (Oct 12, 2021)
12-31287741-T-C			Likely benign (Sep 01, 2022)
12-31287764-T-C		not specified	Uncertain significance (Oct 03, 2022)
12-31293811-G-A		not specified	Uncertain significance (Nov 24, 2024)
12-31293874-T-C		not specified	Uncertain significance (Feb 13, 2024)
12-31293906-C-G		not specified	Uncertain significance (Mar 19, 2024)
12-31293915-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-31295333-T-C		not specified	Likely benign (Nov 29, 2023)
12-31298197-C-A		not specified	Uncertain significance (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SINHCAF	protein_coding	protein_coding	ENST00000337682	5	46475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.965	0.0354	125462	0	1	125463	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	52	115	0.454	0.00000571	1459
Missense in Polyphen		4	21.09	0.18966		290
Synonymous	-0.293	40	37.7	1.06	0.00000172	400
Loss of Function	2.99	0	10.4	0.00	5.88e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Subunit of the Sin3 deacetylase complex (Sin3/HDAC), this subunit is important for the repression of genes encoding components of the TGF-beta signaling pathway (PubMed:22865885, PubMed:22984288). Core component of a SIN3A complex (composed of at least SINHCAF, SIN3A, HDAC1, SAP30, RBBP4, OGT and TET1) present in embryonic stem (ES) cells. Promotes the stability of SIN3A and its presence on chromatin and is essential for maintaining the potential of ES cells to proliferate rapidly, while ensuring a short G1-phase of the cell cycle, thereby preventing premature lineage priming (By similarity). {ECO:0000250|UniProtKB:Q8C8M1, ECO:0000269|PubMed:22865885, ECO:0000269|PubMed:22984288}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.846
• hipred: Y
• hipred_score: 0.673
• ghis: 0.578

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Sinhcaf

Gene ontology

• Biological process: positive regulation of cell population proliferation;negative regulation of cell migration;negative regulation of cell differentiation
• Cellular component: Sin3 complex
• Molecular function: protein binding