FAAP24

FA core complex associated protein 24

Basic information

Region (hg38): 19:32972209-32978229

Previous symbols: [ "C19orf40" ]

Links

ENSG00000131944 ∙ NCBI:91442 ∙ OMIM:610884 ∙ HGNC:28467 ∙ Uniprot:Q9BTP7 ∙ 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 FAAP24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAAP24 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	3	4
missense			17	1	4	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	17	2	10

Variants in FAAP24

This is a list of pathogenic ClinVar variants found in the FAAP24 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32973142-A-G		not specified	Benign (Nov 12, 2023)
19-32973209-C-G		not specified	Uncertain significance (Aug 11, 2024)
19-32973213-C-T		not specified	Uncertain significance (Feb 13, 2024)
19-32973217-T-C		FAAP24-related disorder	Likely benign (Jul 01, 2019)
19-32973225-G-C			Benign (Dec 31, 2019)
19-32973230-G-A		not specified	Likely benign (Jun 28, 2024)
19-32973239-C-A		not specified	Uncertain significance (Jul 16, 2021)
19-32973239-C-G		not specified	Uncertain significance (Oct 16, 2024)
19-32973261-A-T		not specified	Uncertain significance (Oct 06, 2022)
19-32973319-C-T		not specified	Benign (Jan 24, 2024)
19-32974099-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-32974100-G-A		FAAP24-related disorder	Benign (Apr 17, 2018)
19-32974128-A-G			Likely benign (-)
19-32974132-A-G		not specified	Uncertain significance (Oct 06, 2023)
19-32974146-G-A		FAAP24-related disorder	Likely benign (Feb 01, 2024)
19-32974171-G-C		not specified	Uncertain significance (Jul 19, 2023)
19-32974193-C-T		FAAP24-related disorder	Benign (Dec 31, 2019)
19-32974208-A-C		not specified	Uncertain significance (Jun 06, 2023)
19-32974222-G-A		FAAP24-related disorder	Likely benign (Jul 01, 2019)
19-32976450-A-G		not specified	Uncertain significance (Sep 16, 2021)
19-32976451-G-A		not specified	Benign (Nov 12, 2023)
19-32976473-G-C		not specified	Likely benign (Feb 07, 2025)
19-32976516-G-A		not specified	Uncertain significance (Jan 29, 2025)
19-32976560-C-T		not specified	Uncertain significance (Jun 10, 2022)
19-32976563-C-G		not specified	Uncertain significance (Apr 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAAP24	protein_coding	protein_coding	ENST00000588258	4	6014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.21e-8	0.0953	125695	0	52	125747	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.164	118	123	0.958	0.00000693	1384
Missense in Polyphen		33	31.436	1.0497		403
Synonymous	-1.10	63	52.8	1.19	0.00000325	438
Loss of Function	-0.437	10	8.61	1.16	4.29e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000510	0.000449
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000273	0.000273
Middle Eastern	0.000326	0.000326
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in DNA repair through recruitment of the FA core complex to damaged DNA. Regulates FANCD2 monoubiquitination upon DNA damage. Induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. Targets FANCM/FAAP24 complex to the DNA, preferentially to single strand DNA. {ECO:0000269|PubMed:17289582}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Fanconi Anemia Pathway;DNA Repair;Fanconi anemia pathway (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• rvis_EVS: 0.99
• rvis_percentile_EVS: 90.56

Haploinsufficiency Scores

• pHI: 0.0434
• hipred: Y
• hipred_score: 0.537
• ghis: 0.411

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Faap24

Gene ontology

• Biological process: interstrand cross-link repair
• Cellular component: nucleoplasm;intracellular membrane-bounded organelle;Fanconi anaemia nuclear complex
• Molecular function: DNA binding;chromatin binding;protein binding