SINHCAF
protein-codingSIN3-HDAC complex associated factor
Gene summary
Involved in negative regulation of cell migration. Part of Sin3-type complex. [provided by Alliance of Genome Resources, Jul 2025]
- C12orf14
- FAM60A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~46.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SINHCAF variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001135812.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 23 | 2 | 0 | 25 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001129284.1 | 5 | MANE Select | |
| Ensembl | ENSP00000337477.4 | 5 | MANE Select | |
| RefSeq | NP_001129283.1 | 5 | Standard | |
| RefSeq | NP_067061.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of cell population proliferation
- negative regulation of cell migration
- negative regulation of cell differentiation
Molecular Function
- protein binding
Cellular Component
- Sin3 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000337682
- Coding exons
- 5
- Length
- 46475
- Individuals with no LoFs
- 125462
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125463
- p
- 0.00000399
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.08 | 52 | 115 | 0.454 | 0.00000571 | 1459 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (gene trap)
- E