FRAT2

FRAT regulator of WNT signaling pathway 2

Basic information

Region (hg38): 10:97332497-97334729

Links

ENSG00000181274 ∙ NCBI:23401 ∙ OMIM:605006 ∙ HGNC:16048 ∙ Uniprot:O75474 ∙ 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 FRAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRAT2 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			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	2

Variants in FRAT2

This is a list of pathogenic ClinVar variants found in the FRAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-97333935-C-T		not specified	Uncertain significance (Sep 27, 2021)
10-97333941-G-C		not specified	Uncertain significance (Feb 13, 2023)
10-97334029-G-A		not specified	Uncertain significance (Jun 17, 2024)
10-97334092-G-A		not specified	Uncertain significance (Oct 25, 2023)
10-97334092-G-C		not specified	Uncertain significance (Aug 01, 2024)
10-97334094-T-C		not specified	Uncertain significance (Oct 07, 2024)
10-97334109-G-C		not specified	Uncertain significance (Jan 23, 2025)
10-97334122-C-T		not specified	Uncertain significance (Jan 10, 2022)
10-97334161-T-G		not specified	Uncertain significance (Sep 17, 2021)
10-97334173-C-G		not specified	Uncertain significance (Jan 27, 2022)
10-97334194-G-A		not specified	Uncertain significance (Aug 05, 2024)
10-97334200-C-G		not specified	Uncertain significance (Aug 11, 2022)
10-97334207-G-A			Benign (Dec 31, 2019)
10-97334209-G-T		not specified	Uncertain significance (Apr 17, 2024)
10-97334218-C-T		not specified	Uncertain significance (Apr 08, 2022)
10-97334227-C-T		not specified	Uncertain significance (Feb 25, 2025)
10-97334253-G-A		not specified	Uncertain significance (Aug 28, 2024)
10-97334256-G-A		not specified	Uncertain significance (Mar 28, 2023)
10-97334268-G-A		not specified	Uncertain significance (Dec 21, 2023)
10-97334272-C-G		not specified	Uncertain significance (Jan 23, 2024)
10-97334289-A-G		not specified	Uncertain significance (Jan 21, 2025)
10-97334311-G-C		not specified	Uncertain significance (Oct 20, 2023)
10-97334326-C-T			Benign (Dec 31, 2019)
10-97334361-A-C		not specified	Uncertain significance (Sep 16, 2021)
10-97334383-A-C		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRAT2	protein_coding	protein_coding	ENST00000371019	1	2204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0480	0.698	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.414	61	70.8	0.861	0.00000326	1371
Missense in Polyphen		30	35.144	0.85364		617
Synonymous	0.201	32	33.5	0.956	0.00000163	552
Loss of Function	0.627	2	3.21	0.623	1.44e-7	47

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.
• 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 Signaling Pathway;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;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 (Consensus)

Recessive Scores

• pRec: 0.138

Haploinsufficiency Scores

• pHI: 0.741
• hipred: Y
• hipred_score: 0.557
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.642

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Frat2
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development;cell population proliferation;beta-catenin destruction complex disassembly
• Cellular component: cellular_component;cytosol
• Molecular function: molecular_function