FOXR1

forkhead box R1, the group of Forkhead boxes

Basic information

Region (hg38): 11:118971712-118981287

Links

ENSG00000176302 ∙ NCBI:283150 ∙ OMIM:615755 ∙ HGNC:29980 ∙ Uniprot:Q6PIV2 ∙ 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 FOXR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXR1 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			17	1		18
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	1	1

Variants in FOXR1

This is a list of pathogenic ClinVar variants found in the FOXR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118978977-C-G		not specified	Uncertain significance (Dec 17, 2021)
11-118978977-C-T		not specified	Uncertain significance (Feb 23, 2025)
11-118979003-T-C			Benign (Dec 26, 2018)
11-118979038-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-118979121-G-A		not specified	Likely benign (Feb 21, 2024)
11-118979132-A-C		not specified	Uncertain significance (May 04, 2023)
11-118979161-C-G		not specified	Uncertain significance (Feb 05, 2024)
11-118979167-C-T		not specified	Uncertain significance (Jul 31, 2024)
11-118979518-C-G		not specified	Uncertain significance (Dec 21, 2022)
11-118979530-G-T		not specified	Uncertain significance (Dec 17, 2024)
11-118979539-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-118980509-C-T		not specified	Uncertain significance (Dec 15, 2023)
11-118980513-C-T		not specified	Uncertain significance (Oct 20, 2021)
11-118980519-C-G		not specified	Uncertain significance (Jan 23, 2024)
11-118980519-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-118980560-C-G		not specified	Uncertain significance (Oct 07, 2024)
11-118980579-T-C		not specified	Uncertain significance (Apr 19, 2024)
11-118980592-G-A		not specified	Uncertain significance (Apr 25, 2023)
11-118980596-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-118980612-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-118980653-C-A		not specified	Uncertain significance (May 20, 2024)
11-118980692-C-T		not specified	Uncertain significance (Feb 22, 2025)
11-118980716-A-T			Uncertain significance (Aug 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXR1	protein_coding	protein_coding	ENST00000317011	6	9585

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000155	0.654	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.156	167	173	0.967	0.00000998	1892
Missense in Polyphen		47	53.867	0.87251		661
Synonymous	1.31	52	65.5	0.793	0.00000350	572
Loss of Function	1.04	11	15.4	0.713	9.53e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000238	0.000238
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000279	0.000277
European (Non-Finnish)	0.000320	0.000316
Middle Eastern	0.0000544	0.0000544
South Asian	0.000262	0.000261
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.359
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.0997
• hipred: N
• hipred_score: 0.158

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Foxr1

Gene ontology

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