FRAT2

protein-coding

FRAT regulator of WNT signaling pathway 2

Gene summary

The protein encoded by this intronless gene belongs to the GSK-3-binding protein family. Studies show that this protein plays a role as a positive regulator of the WNT signaling pathway. It may be upregulated in tumor progression. [provided by RefSeq, Jul 2008]

MANE transcript

NM_012083.3

Inheritance

—

ClinVar variants

U:42B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr10:97,332,497-97,334,729

External References & Databases

Ensembl (ENSG00000181274)

Transcript & Mutation Effects

hg38 • Region Span ~2.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FRAT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012083.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			42 clinvar	1 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	1	1	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012083.3	RefSeq	NP_036215.1	1	MANE Select
ENST00000371019.4	Ensembl	ENSP00000360058.2	1	MANE Select
ENST00001122580.1	Ensembl	ENSP00000792385.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

multicellular organism development
cell population proliferation
beta-catenin destruction complex disassembly

Molecular Function

molecular_function

Cellular Component

cellular_component
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371019
Coding exons: 1
Length: 2204
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.414	61	70.8	0.861	0.00000326	1371
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Positively regulates the Wnt signaling pathway by stabilizing beta-catenin through the association with GSK-3.;

Recessive Scores

pRec: 0.138

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.642

Gene Damage Prediction

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