FATE1

fetal and adult testis expressed 1

Basic information

Region (hg38): X:151716035-151723194

Links

ENSG00000147378 ∙ NCBI:89885 ∙ OMIM:300450 ∙ HGNC:24683 ∙ Uniprot:Q969F0 ∙ 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 FATE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FATE1 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		1
missense			17	4		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	5	0

Variants in FATE1

This is a list of pathogenic ClinVar variants found in the FATE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-151716160-T-A		not specified	Uncertain significance (Dec 04, 2024)
X-151716212-C-A		not specified	Uncertain significance (May 13, 2022)
X-151717293-G-A		not specified	Likely benign (Dec 01, 2022)
X-151717362-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-151721417-G-C		not specified	Uncertain significance (Mar 23, 2022)
X-151721426-G-C		not specified	Uncertain significance (Jan 15, 2025)
X-151721458-G-C		not specified	Uncertain significance (Mar 01, 2024)
X-151721459-A-G		not specified	Uncertain significance (Jun 25, 2024)
X-151721480-G-A		not specified	Uncertain significance (Nov 17, 2022)
X-151721485-C-T		not specified	Uncertain significance (Nov 08, 2022)
X-151721486-G-A			Likely benign (Jul 20, 2018)
X-151721910-G-C		not specified	Uncertain significance (Dec 24, 2024)
X-151721926-C-T		not specified	Uncertain significance (Feb 07, 2025)
X-151721950-A-G		not specified	Uncertain significance (Dec 02, 2022)
X-151721952-G-A		not specified	Uncertain significance (Dec 21, 2024)
X-151722631-T-C		not specified	Uncertain significance (Jul 26, 2021)
X-151722673-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-151722676-A-T		not specified	Uncertain significance (Oct 02, 2023)
X-151722682-C-A		not specified	Uncertain significance (Feb 22, 2023)
X-151722683-G-A		not specified	Uncertain significance (Mar 24, 2023)
X-151722689-G-A		not specified	Likely benign (Jan 19, 2022)
X-151722709-G-C		not specified	Likely benign (Mar 01, 2023)
X-151722712-C-T			Likely benign (Sep 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FATE1	protein_coding	protein_coding	ENST00000370350	5	7160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00717	0.782	125641	12	29	125682	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.338	87	78.6	1.11	0.00000649	1184
Missense in Polyphen		24	17.235	1.3925		315
Synonymous	0.135	28	28.9	0.968	0.00000226	361
Loss of Function	0.950	4	6.64	0.602	5.56e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00142	0.00142
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000221	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of endoplasmic reticulum (ER)-mitochondria coupling. Negatively regulates the ER- mitochondria distance and Ca(2+) transfer from ER to mitochondria possibly implicating it in the regulation of apoptosis (PubMed:27402544). May collaborate with RNF183 to restrain BIK protein levels thus regulating apoptotic signaling (PubMed:26567849). {ECO:0000269|PubMed:27402544, ECO:0000305|PubMed:26567849}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.494
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.0844
• hipred: N
• hipred_score: 0.123
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.708

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fate1

Gene ontology

• Biological process: apoptotic process;negative regulation of apoptotic process;negative regulation of mitochondrial calcium ion concentration
• Cellular component: mitochondrial outer membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;mitochondria-associated endoplasmic reticulum membrane
• Molecular function: protein binding;ubiquitin protein ligase binding