RHOXF2B

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

Basic information

Region (hg38): X:120072264-120077690

Links

ENSG00000203989 ∙ NCBI:727940 ∙ ∙ HGNC:33519 ∙ Uniprot:P0C7M4 ∙ 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 RHOXF2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOXF2B 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	3	0

Variants in RHOXF2B

This is a list of pathogenic ClinVar variants found in the RHOXF2B 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-120075904-A-C		not specified	Uncertain significance (Aug 23, 2021)
X-120076957-G-A			Likely benign (May 01, 2022)
X-120076964-T-G		not specified	Uncertain significance (Dec 28, 2023)
X-120076998-C-T		not specified	Uncertain significance (Jul 31, 2024)
X-120077046-C-T		not specified	Uncertain significance (Aug 11, 2024)
X-120077048-C-T		not specified	Uncertain significance (Nov 08, 2024)
X-120077100-A-T		not specified	Uncertain significance (Aug 11, 2024)
X-120077108-C-T		not specified	Uncertain significance (Nov 29, 2023)
X-120077118-C-T		not specified	Uncertain significance (Apr 28, 2022)
X-120077121-C-T		not specified	Uncertain significance (Apr 25, 2023)
X-120077122-GCCGCCGCCATCTTTTTCTTCT-G			Likely benign (Apr 01, 2023)
X-120077124-C-T			Likely benign (Feb 01, 2023)
X-120077148-C-T		not specified	Uncertain significance (Dec 21, 2023)
X-120077217-C-T		not specified	Uncertain significance (Mar 19, 2024)
X-120077267-G-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOXF2B	protein_coding	protein_coding	ENST00000371402	4	5860

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.251	0.650	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0734	56	54.5	1.03	0.00000493	1895
Missense in Polyphen		11	10.342	1.0636		485
Synonymous	-0.331	31	28.7	1.08	0.00000315	540
Loss of Function	1.21	1	3.42	0.292	2.17e-7	106

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

• 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}.

Haploinsufficiency Scores

• pHI: 0.0454
• hipred: N
• hipred_score: 0.187
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 5.13e-11

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

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;sequence-specific DNA binding