RHOXF2

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

Basic information

Region (hg38): X:120158613-120165630

Links

ENSG00000131721 ∙ NCBI:84528 ∙ OMIM:300447 ∙ HGNC:30011 ∙ Uniprot:Q9BQY4 ∙ 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 RHOXF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOXF2 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				3		3
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	0

Variants in RHOXF2

This is a list of pathogenic ClinVar variants found in the RHOXF2 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-120159121-G-A			Likely benign (Aug 01, 2022)
X-120159141-A-C		not specified	Uncertain significance (Jul 20, 2021)
X-120159158-G-A		not specified	Uncertain significance (May 25, 2022)
X-120159185-G-A		not specified	Uncertain significance (May 20, 2024)
X-120159217-C-T			Likely benign (Oct 01, 2022)
X-120159230-G-A		not specified	Conflicting classifications of pathogenicity (Dec 01, 2022)
X-120159268-G-T		not specified	Uncertain significance (Apr 07, 2023)
X-120159302-G-A		not specified	Uncertain significance (Apr 22, 2022)
X-120159305-G-A		not specified	Uncertain significance (Jun 27, 2022)
X-120159308-G-A		not specified	Uncertain significance (May 14, 2024)
X-120159326-G-A		not specified	Uncertain significance (Nov 20, 2023)
X-120159332-G-A		not specified	Uncertain significance (Sep 06, 2022)
X-120159345-A-G		not specified	Likely benign (May 24, 2024)
X-120159346-C-T			Likely benign (Oct 01, 2022)
X-120159350-C-T			Likely benign (-)
X-120159371-C-G		not specified	Uncertain significance (Mar 04, 2024)
X-120159425-C-G		not specified	Uncertain significance (Dec 21, 2023)
X-120163624-A-G		not specified	Likely benign (Aug 19, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOXF2	protein_coding	protein_coding	ENST00000371388	4	5479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000218	0.312	123203	2	564	123769	0.00229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.125	63	65.8	0.957	0.00000611	1874
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00186	0.00151
Ashkenazi Jewish	0.000732	0.000498
East Asian	0.00	0.00
Finnish	0.00494	0.00307
European (Non-Finnish)	0.00728	0.00403
Middle Eastern	0.00	0.00
South Asian	0.000360	0.000197
Other	0.00318	0.00197

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0212
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 4.65e-10

Gene Damage Prediction

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

Gene ontology

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