FAAP20
protein-codingFA core complex associated protein 20
Gene summary
Enables K63-linked polyubiquitin modification-dependent protein binding activity and ubiquitin-modified protein reader activity. Involved in interstrand cross-link repair and translesion synthesis. Located in chromatin and nuclear body. Part of Fanconi anaemia nuclear complex. [provided by Alliance of Genome Resources, Jun 2026]
- C1orf86
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.3 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 FAAP20 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_182533.4. 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 | 8 | 3 | 11 | |||
| missense | 7 | 4 | 11 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 17 | 7 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_872339.3 | 4 | MANE Select | |
| Ensembl | ENSP00000367808.4 | 4 | MANE Select | |
| RefSeq | NP_001139782.1 | 4 | Standard | |
| RefSeq | NP_001243874.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fanconi Anemia Pathway
- DNA Repair
Biological Process
- cellular response to DNA damage stimulus
- translesion synthesis
- interstrand cross-link repair
Molecular Function
- protein binding
- polyubiquitin modification-dependent protein binding
- ubiquitin binding
- metal ion binding
- K63-linked polyubiquitin modification-dependent protein binding
Cellular Component
- nucleoplasm
- chromosome
- nuclear body
- cell junction
- Fanconi anaemia nuclear complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378546
- Coding exons
- 4
- Length
- 28257
- Individuals with no LoFs
- 125209
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125216
- p
- 0.0000280
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.198 | 102 | 108 | 0.946 | 0.00000711 | 1098 |
| Missense (PolyPhen) | 40 | 38.073 | 1.0506 | 287 | ||
| Synonymous | -0.768 | 59 | 52.0 | 1.14 | 0.00000365 | 399 |
| Loss of Function | 1.96 | 1 | 6.32 | 0.158 | 2.71e-7 | 70 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000069 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000091 | 0.0000089 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the Fanconi anemia (FA) complex required to recruit the FA complex to DNA interstrand cross-links (ICLs) and promote ICLs repair. Following DNA damage recognizes and binds 'Lys-63'-linked ubiquitin generated by RNF8 at ICLs and recruits other components of the FA complex. Promotes translesion synthesis via interaction with REV1. {ECO:0000269|PubMed:22266823, ECO:0000269|PubMed:22343915, ECO:0000269|PubMed:22396592, ECO:0000269|PubMed:22705371}.;
Intolerance Scores
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.12
Essentials
- Essential (gene trap)
- N