FAAP20

FA core complex associated protein 20

Basic information

Region (hg38): 1:2184461-2212720

Previous symbols: [ "C1orf86" ]

Links

ENSG00000162585 ∙ NCBI:199990 ∙ OMIM:615183 ∙ HGNC:26428 ∙ Uniprot:Q6NZ36 ∙ 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 FAAP20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAAP20 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			4	2		6
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	2
Total	0	0	7	3	1

Variants in FAAP20

This is a list of pathogenic ClinVar variants found in the FAAP20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2184675-C-G			Likely benign (Jul 01, 2022)
1-2184994-C-T			Benign (Dec 31, 2019)
1-2193680-G-C		not specified	Uncertain significance (Jan 30, 2024)
1-2193702-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-2193744-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-2193794-G-A		not specified	Uncertain significance (Jun 03, 2024)
1-2193833-C-T		not specified	Likely benign (Aug 08, 2022)
1-2193836-C-T		not specified	Likely benign (Oct 03, 2022)
1-2193869-G-A		not specified	Uncertain significance (Nov 05, 2021)
1-2193893-C-T		not specified	Uncertain significance (Aug 28, 2023)
1-2193896-G-A		not specified	Uncertain significance (Aug 30, 2022)
1-2193908-C-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAAP20	protein_coding	protein_coding	ENST00000378546	4	28257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.526	0.460	125209	0	7	125216	0.0000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.198	102	108	0.946	0.00000711	1098
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000692	0.0000620
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000908	0.00000885
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Fanconi Anemia Pathway;DNA Repair (Consensus)

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.0645
• hipred: Y
• hipred_score: 0.508
• ghis: 0.645

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Faap20
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cellular response to DNA damage stimulus;translesion synthesis;interstrand cross-link repair
• Cellular component: nucleoplasm;chromosome;nuclear body;cell junction;Fanconi anaemia nuclear complex
• Molecular function: protein binding;polyubiquitin modification-dependent protein binding;ubiquitin binding;metal ion binding;K63-linked polyubiquitin modification-dependent protein binding;ubiquitin-dependent protein binding