FAF1

Fas associated factor 1, the group of UBX domain containing

Basic information

Region (hg38): 1:50437027-50960267

Links

ENSG00000185104 ∙ NCBI:11124 ∙ OMIM:604460 ∙ HGNC:3578 ∙ Uniprot:Q9UNN5 ∙ 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 FAF1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAF1 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						0
missense			17			17
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	17	0	0

Variants in FAF1

This is a list of pathogenic ClinVar variants found in the FAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-50475675-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-50491713-A-C			Benign (Mar 29, 2018)
1-50539663-G-A		not specified	Uncertain significance (Jun 27, 2022)
1-50539676-G-A		not specified	Uncertain significance (Feb 26, 2024)
1-50567089-G-T		not specified	Uncertain significance (Jul 14, 2022)
1-50567196-T-G		not specified	Uncertain significance (Aug 11, 2022)
1-50567216-T-C		not specified	Uncertain significance (Dec 21, 2022)
1-50582622-C-T		not specified	Uncertain significance (Jun 06, 2023)
1-50582648-A-T		not specified	Uncertain significance (Jul 15, 2021)
1-50584688-T-A		not specified	Uncertain significance (Dec 20, 2023)
1-50584706-C-A		not specified	Uncertain significance (Sep 20, 2023)
1-50584711-G-A		not specified	Uncertain significance (Jun 12, 2023)
1-50584742-C-G		not specified	Uncertain significance (Dec 13, 2023)
1-50584800-A-T		not specified	Uncertain significance (Jan 02, 2024)
1-50596142-C-G		not specified	Uncertain significance (Aug 11, 2022)
1-50596156-A-G		not specified	Uncertain significance (Dec 02, 2021)
1-50596206-G-C		not specified	Uncertain significance (Apr 14, 2022)
1-50705839-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-50738915-G-C		not specified	Uncertain significance (Dec 18, 2023)
1-50738918-T-C		not specified	Uncertain significance (Nov 09, 2022)
1-50744758-G-C		not specified	Uncertain significance (Dec 21, 2022)
1-50788003-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-50788015-C-G		not specified	Uncertain significance (Jun 13, 2023)
1-50788029-T-A		not specified	Uncertain significance (Jun 26, 2023)
1-50788074-G-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAF1	protein_coding	protein_coding	ENST00000396153	19	520786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00105	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.13	246	359	0.684	0.0000195	4273
Missense in Polyphen		45	95.515	0.47113		1074
Synonymous	1.27	107	125	0.855	0.00000669	1202
Loss of Function	5.29	5	41.9	0.119	0.00000227	480

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000199	0.0000992
East Asian	0.00	0.00
Finnish	0.0000931	0.0000924
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-binding protein (PubMed:19722279). Required for the progression of DNA replication forks by targeting DNA replication licensing factor CDT1 for degradation (PubMed:26842564). Potentiates but cannot initiate FAS-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:P54731, ECO:0000269|PubMed:19722279, ECO:0000269|PubMed:26842564}.
• Pathway: Necroptosis - Homo sapiens (human);Retinoblastoma (RB) in Cancer;Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation;VEGFA-VEGFR2 Signaling Pathway;fas signaling pathway (cd95);TNFalpha (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.189
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.400
• hipred: Y
• hipred_score: 0.786
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Faf1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: faf1
• Affected structure: ceratobranchial cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: apoptotic process;cytoplasmic sequestering of NF-kappaB;cell death;positive regulation of cell death;regulation of cell adhesion;positive regulation of protein complex assembly;regulation of protein catabolic process;positive regulation of apoptotic process;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of DNA replication;regulation of protein kinase activity;positive regulation of extrinsic apoptotic signaling pathway via death domain receptors;positive regulation of cellular protein catabolic process
• Cellular component: nucleus;nuclear envelope;cytosol;CD95 death-inducing signaling complex;VCP-NPL4-UFD1 AAA ATPase complex;perinuclear region of cytoplasm
• Molecular function: protein binding;protein kinase regulator activity;protein kinase binding;protein domain specific binding;heat shock protein binding;ubiquitin protein ligase binding;ubiquitin binding;NF-kappaB binding