FOXR2

forkhead box R2, the group of Forkhead boxes

Basic information

Region (hg38): X:55623400-55626192

Links

ENSG00000189299 ∙ NCBI:139628 ∙ OMIM:300949 ∙ HGNC:30469 ∙ Uniprot:Q6PJQ5 ∙ 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 FOXR2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXR2 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				2		2
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	3	0

Variants in FOXR2

This is a list of pathogenic ClinVar variants found in the FOXR2 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-55623746-A-G		not specified	Uncertain significance (Mar 06, 2025)
X-55623850-G-A		not specified	Uncertain significance (Aug 12, 2021)
X-55623865-G-A		not specified	Likely benign (Jul 08, 2021)
X-55623866-G-T		not specified	Uncertain significance (Apr 25, 2023)
X-55623875-A-C		not specified	Uncertain significance (Feb 27, 2025)
X-55623991-G-A		not specified	Uncertain significance (Aug 09, 2021)
X-55624010-G-C		not specified	Uncertain significance (Oct 13, 2023)
X-55624076-G-C		not specified	Uncertain significance (Feb 05, 2024)
X-55624093-G-T		not specified	Uncertain significance (May 26, 2024)
X-55624105-C-T		not specified	Uncertain significance (Jun 12, 2023)
X-55624110-T-C			Likely benign (Jun 01, 2022)
X-55624226-T-C		not specified	Uncertain significance (Feb 04, 2025)
X-55624267-C-G		not specified	Uncertain significance (May 03, 2023)
X-55624276-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-55624335-C-A		not specified	Uncertain significance (Aug 11, 2024)
X-55624361-A-G		not specified	Uncertain significance (Dec 13, 2023)
X-55624396-T-C		not specified	Uncertain significance (May 06, 2024)
X-55624450-C-A		not specified	Uncertain significance (Dec 17, 2024)
X-55624473-A-T			Likely benign (Mar 01, 2022)
X-55624474-G-C		not specified	Uncertain significance (Aug 19, 2024)
X-55624493-A-T		not specified	Uncertain significance (Dec 23, 2023)
X-55624543-C-A		not specified	Uncertain significance (Nov 27, 2024)
X-55624544-G-A		not specified	Uncertain significance (Sep 24, 2024)
X-55624546-C-T		not specified	Uncertain significance (Sep 26, 2022)
X-55624547-G-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXR2	protein_coding	protein_coding	ENST00000339140	1	2789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0767	0.555	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.212	119	113	1.06	0.00000792	2084
Missense in Polyphen		26	30.49	0.85274		601
Synonymous	-1.15	52	42.5	1.22	0.00000301	564
Loss of Function	-0.379	1	0.667	1.50	4.20e-8	12

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

Recessive Scores

• pRec: 0.0927

Intolerance Scores

• loftool: 0.367
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxr2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding