RHOXF1

Rhox homeobox family member 1, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): X:120109051-120245267

Links

ENSG00000101883 ∙ NCBI:158800 ∙ OMIM:300446 ∙ HGNC:29993 ∙ Uniprot:Q8NHV9 ∙ 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 RHOXF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHOXF1 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			7	2	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11	4		15
Total	0	0	18	6	2

Variants in RHOXF1

This is a list of pathogenic ClinVar variants found in the RHOXF1 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-120109203-C-T		not specified	Likely benign (Mar 05, 2024)
X-120109219-G-T		not specified	Uncertain significance (Oct 02, 2023)
X-120109232-C-T			Benign (Dec 31, 2019)
X-120109268-C-T		not specified	Uncertain significance (Dec 28, 2023)
X-120109275-A-G		not specified	Uncertain significance (Sep 14, 2022)
X-120112897-T-G		not specified	Uncertain significance (May 01, 2024)
X-120115468-G-T		not specified	Uncertain significance (Sep 23, 2023)
X-120115580-C-T		not specified	Uncertain significance (Feb 15, 2023)
X-120115635-C-T			Benign (Dec 31, 2019)
X-120115667-T-C		not specified	Likely benign (Dec 22, 2023)
X-120115729-A-G		not specified	Uncertain significance (Jul 09, 2021)
X-120115834-A-G		not specified	Uncertain significance (Nov 12, 2021)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHOXF1	protein_coding	protein_coding	ENST00000217999	3	6837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.775	0.218	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0789	92	89.9	1.02	0.00000853	1198
Missense in Polyphen		12	13.907	0.86288		191
Synonymous	0.227	36	37.8	0.953	0.00000400	357
Loss of Function	2.06	0	4.94	0.00	4.50e-7	64

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}.

Recessive Scores

• pRec: 0.0412

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.00918
• hipred: N
• hipred_score: 0.183
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

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, DNA-templated;regulation of transcription by RNA polymerase II;multicellular organism development;gamete generation;positive regulation of gene expression;sexual reproduction;intracellular steroid hormone receptor signaling pathway
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;sequence-specific DNA binding