FRAT1

FRAT regulator of WNT signaling pathway 1

Basic information

Region (hg38): 10:97319271-97321915

Links

ENSG00000165879 ∙ NCBI:10023 ∙ OMIM:602503 ∙ HGNC:3944 ∙ Uniprot:Q92837 ∙ 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 FRAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRAT1 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in FRAT1

This is a list of pathogenic ClinVar variants found in the FRAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97319481-G-A		not specified	Uncertain significance (Nov 10, 2024)
10-97319519-G-C		not specified	Uncertain significance (Sep 01, 2021)
10-97319613-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-97319632-C-G		not specified	Uncertain significance (Aug 17, 2022)
10-97319655-G-A		not specified	Uncertain significance (Jul 25, 2023)
10-97319677-G-A		not specified	Uncertain significance (Nov 22, 2023)
10-97319694-G-A		not specified	Uncertain significance (Jun 18, 2024)
10-97319698-C-G		not specified	Uncertain significance (Jul 31, 2024)
10-97319706-A-C		not specified	Uncertain significance (Oct 28, 2024)
10-97319709-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-97319722-C-A		not specified	Uncertain significance (Nov 30, 2022)
10-97319775-C-G		not specified	Uncertain significance (Sep 26, 2024)
10-97319823-C-T		not specified	Uncertain significance (Jun 24, 2022)
10-97319847-G-C		not specified	Uncertain significance (May 08, 2024)
10-97319974-G-A		not specified	Uncertain significance (May 11, 2022)
10-97319997-C-G		not specified	Uncertain significance (Nov 07, 2022)
10-97320181-C-G		not specified	Uncertain significance (Nov 24, 2024)
10-97320187-A-T		not specified	Uncertain significance (Mar 20, 2024)
10-97320193-C-A		not specified	Uncertain significance (Jan 24, 2023)
10-97320228-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-97320262-C-A		not specified	Uncertain significance (Dec 10, 2024)
10-97320267-G-A		not specified	Uncertain significance (Feb 21, 2024)
10-97320273-G-A		not specified	Uncertain significance (Aug 28, 2024)
10-97320285-G-C		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRAT1	protein_coding	protein_coding	ENST00000371021	1	2651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.323	0.616	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.230	93	99.4	0.935	0.00000455	1657
Missense in Polyphen		30	40.235	0.74561		661
Synonymous	0.922	39	47.0	0.829	0.00000220	674
Loss of Function	1.46	1	4.24	0.236	1.83e-7	56

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates the Wnt signaling pathway by stabilizing beta-catenin through the association with GSK-3. May play a role in tumor progression and collaborate with PIM1 and MYC in lymphomagenesis. {ECO:0000269|PubMed:12556519}.
• Pathway: Gastric cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);WNT-Core;Wnt Signaling Pathway;Wnt Signaling Pathway and Pluripotency;Wnt Signaling Pathway;DNA Damage Response (only ATM dependent);Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;wnt signaling pathway;multi-step regulation of transcription by pitx2;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Disassembly of the destruction complex and recruitment of AXIN to the membrane;Beta-catenin phosphorylation cascade;Wnt Canonical;TCF dependent signaling in response to WNT;Wnt Mammals;Presenilin action in Notch and Wnt signaling (Consensus)

Recessive Scores

• pRec: 0.170

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.465
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frat1
• Phenotype: normal phenotype

Gene ontology

• Biological process: canonical Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway;beta-catenin destruction complex disassembly
• Cellular component: cytoplasm;cytosol;intracellular membrane-bounded organelle
• Molecular function: protein binding