XAF1

XIAP associated factor 1, the group of Zinc fingers TRAF-type

Basic information

Region (hg38): 17:6755447-6775647

Links

ENSG00000132530

∙ NCBI:54739 ∙ OMIM:606717 ∙ HGNC:30932 ∙ Uniprot:Q6GPH4 ∙ 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 XAF1 gene.

not_specified (38 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XAF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017523.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			33 clinvar	5 clinvar	1 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	5	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XAF1	protein_coding	protein_coding	ENST00000361842	7	20201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.82e-12	0.0185	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.106	161	165	0.977	0.00000866	1990
Missense in Polyphen		28	36.765	0.7616		442
Synonymous	-0.489	64	59.2	1.08	0.00000321	521
Loss of Function	-0.491	16	14.0	1.14	5.87e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000549	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000549	0.000544
South Asian	0.000206	0.000196
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to function as a negative regulator of members of the IAP (inhibitor of apoptosis protein) family. Inhibits anti- caspase activity of BIRC4. Induces cleavage and inactivation of BIRC4 independent of caspase activation. Mediates TNF-alpha- induced apoptosis and is involved in apoptosis in trophoblast cells. May inhibit BIRC4 indirectly by activating the mitochondrial apoptosis pathway. After translocation to mitochondria, promotes translocation of BAX to mitochondria and cytochrome c release from mitochondria. Seems to promote the redistribution of BIRC4 from the cytoplasm to the nucleus, probably independent of BIRC4 inactivation which seems to occur in the cytoplasm. The BIRC4-XAF1 complex mediates down-regulation of BIRC5/survivin; the process requires the E3 ligase activity of BIRC4. Seems to be involved in cellular sensitivity to the proapoptotic actions of TRAIL. May be a tumor suppressor by mediating apoptosis resistance of cancer cells. {ECO:0000269|PubMed:11175744, ECO:0000269|PubMed:12029096, ECO:0000269|PubMed:16432762, ECO:0000269|PubMed:17329253, ECO:0000269|PubMed:17613533}.;
Pathway: Copper homeostasis;Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

pRec: 0.0853

Intolerance Scores

loftool: 0.923
rvis_EVS: 1
rvis_percentile_EVS: 90.62

Haploinsufficiency Scores

pHI: 0.0576
hipred: N
hipred_score: 0.352
ghis: 0.399

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0497

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Xaf1
Phenotype

Gene ontology

Biological process: apoptotic process;response to interferon-beta;type I interferon signaling pathway
Cellular component: nucleus;mitochondrion;cytosol
Molecular function: zinc ion binding