RHOXF2

protein-coding

Rhox homeobox family member 2, the group of PRD class homeoboxes and pseudogenes

Gene summary

This gene, which encodes a transcriptional repressor, is one of two paralogous X-linked homeobox-containing genes and is highly expressed in a variety of cancers. In addition, the encoded protein associates with the cell membrane and with microtubules, and is concentrated at the leading edge of migratory cells. [provided by RefSeq, Dec 2015]

MANE transcript

NM_032498.3

Inheritance

—

ClinVar variants

U:23B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.2

Max pathogenic AF

—

Genomic locus

chrX:120,158,613-120,165,630

External References & Databases

Ensembl (ENSG00000131721)

Transcript & Mutation Effects

hg38 • Region Span ~7.0 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 RHOXF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032498.3. 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				3 clinvar		3
missense			23 clinvar	5 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	8	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032498.3	RefSeq	NP_115887.1	4	MANE Select
ENST00000371388.5	Ensembl	ENSP00000360441.3	4	MANE Select
ENST00001094318.1	Ensembl	ENSP00000764124.1	3	Standard
ENST00001133367.1	Ensembl	ENSP00000809865.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
positive regulation of gene expression

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371388
Coding exons: 4
Length: 5479
Individuals with no LoFs: 123203
Homozygous LoFs: 2
Heterozygous LoFs: 564
Defined: 123769
p: 0.00229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.125	63	65.8	0.957	0.00000611	1874
Missense (PolyPhen)		17	20.379	0.8342		637
Synonymous	-1.54	46	34.5	1.33	0.00000388	532
Loss of Function	-0.379	5	4.16	1.20	2.64e-7	103

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00091	0.00056	rare
Latino/Admixed American	0.00095	0.00070	rare
Ashkenazi Jewish	0.00073	0.00050	rare
East Asian	0	0.0	absent
Finnish	0.0049	0.0031	notable
European (Non-Finnish)	0.0073	0.0040	notable
South Asian	0.00036	0.00020	rare
Other	0.0032	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor maybe involved in reproductive processes. Modulates expression of target genes encoding proteins involved in processes relevant to spermatogenesis. {ECO:0000269|PubMed:28171660}.;

Recessive Scores

pRec: 0.0519

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 4.65e-10

Gene Damage Prediction

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