FATE1

fetal and adult testis expressed 1

Basic information

Region (hg38): X:151716035-151723194

Links

ENSG00000147378NCBI:89885OMIM:300450HGNC:24683Uniprot:Q969F0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
17
clinvar
4
clinvar
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)3513397
X-151716212-C-A not specified Uncertain significance (May 13, 2022)2289531
X-151717293-G-A not specified Likely benign (Dec 01, 2022)2357272
X-151717362-G-A not specified Uncertain significance (Feb 16, 2023)2454566
X-151721417-G-C not specified Uncertain significance (Mar 23, 2022)2279689
X-151721426-G-C not specified Uncertain significance (Jan 15, 2025)2361414
X-151721458-G-C not specified Uncertain significance (Mar 01, 2024)3093226
X-151721459-A-G not specified Uncertain significance (Jun 25, 2024)3513399
X-151721480-G-A not specified Uncertain significance (Nov 17, 2022)2311666
X-151721485-C-T not specified Uncertain significance (Nov 08, 2022)2324645
X-151721486-G-A Likely benign (Jul 20, 2018)764896
X-151721910-G-C not specified Uncertain significance (Dec 24, 2024)3849106
X-151721926-C-T not specified Uncertain significance (Feb 07, 2025)2387944
X-151721950-A-G not specified Uncertain significance (Dec 02, 2022)2332143
X-151721952-G-A not specified Uncertain significance (Dec 21, 2024)2375841
X-151722631-T-C not specified Uncertain significance (Jul 26, 2021)2365212
X-151722673-G-A not specified Uncertain significance (Jul 26, 2022)2389186
X-151722676-A-T not specified Uncertain significance (Oct 02, 2023)3093227
X-151722682-C-A not specified Uncertain significance (Feb 22, 2023)2487457
X-151722683-G-A not specified Uncertain significance (Mar 24, 2023)2529501
X-151722689-G-A not specified Likely benign (Jan 19, 2022)2382954
X-151722709-G-C not specified Likely benign (Mar 01, 2023)2492873
X-151722712-C-T Likely benign (Sep 01, 2022)2661649

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FATE1protein_codingprotein_codingENST00000370350 57160
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.007170.78212564112291256820.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3388778.61.110.000006491184
Missense in Polyphen2417.2351.3925315
Synonymous0.1352828.90.9680.00000226361
Loss of Function0.95046.640.6025.56e-795

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001420.00142
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001220.00000880
Middle Eastern0.000.00
South Asian0.000.00
Other0.0002210.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Fate1
Phenotype

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