FOXR1

protein-coding

forkhead box R1, the group of Forkhead boxes

Gene summary

This gene encodes a member of the forkhead box (FOX) family of transcription factors. FOX family members are monomeric, helix-turn-helix proteins with a core DNA-binding domain of approximately 110 aa. Many FOX transcription factors play roles in determining cell fates during early development. This forkhead box protein lacks the C-terminal basic region found in many other FOX family members. It is located within the 11q23.3 region which is commonly deleted in neuroblastomas. [provided by RefSeq, Jul 2008]

MANE transcript

NM_181721.3

Inheritance

ClinVar variants

U:45B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr11:118,971,712-118,981,287

External References & Databases

Ensembl (ENSG00000176302)

Transcript & Mutation Effects

hg38 • Region Span ~9.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FOXR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181721.3. 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 clinvar	2
missense			43 clinvar	3 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	45	3	1	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181721.3	RefSeq	NP_859072.1	6	MANE Select
ENST00000317011.8	Ensembl	ENSP00000314806.3	6	MANE Select
ENST00000531539.5	Ensembl	ENSP00000433394.1	6	Standard
ENST00000533282.1	Ensembl	ENSP00000432358.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317011
Coding exons: 6
Length: 9585
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 60
Defined: 125748
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.156	167	173	0.967	0.00000998	1892
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.00026	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.154

Intolerance Scores

LoFtool: 0.359
RVIS EVS: 0.15
RVIS percentile EVS: 64.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.260

Gene Damage Prediction

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