RHBDF1

rhomboid 5 homolog 1, the group of Rhomboid family

Basic information

Region (hg38): 16:58059-76355

Previous symbols: [ "C16orf8" ]

Links

ENSG00000007384 ∙ NCBI:64285 ∙ OMIM:614403 ∙ HGNC:20561 ∙ Uniprot:Q96CC6 ∙ 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 RHBDF1 gene.

• not_specified (140 variants)
• not_provided (12 variants)
• Wolff-Parkinson-White_pattern (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022450.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	4	5	10
missense			148	3	2	153
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	153	7	7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHBDF1	protein_coding	protein_coding	ENST00000262316	17	18297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	481	579	0.830	0.0000416	5532
Missense in Polyphen		181	227.53	0.79551		2178
Synonymous	-0.0322	243	242	1.00	0.0000180	1703
Loss of Function	1.89	29	42.3	0.686	0.00000220	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000109	0.000109
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000319	0.000308
Middle Eastern	0.000109	0.000109
South Asian	0.000328	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rhomboid protease-like protein which has no protease activity but regulates the secretion of several ligands of the epidermal growth factor receptor. Indirectly activates the epidermal growth factor receptor signaling pathway and may thereby regulate sleep, cell survival, proliferation and migration. {ECO:0000269|PubMed:15965977, ECO:0000269|PubMed:18524845, ECO:0000269|PubMed:18832597, ECO:0000269|PubMed:21439629}.

Intolerance Scores

• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.6

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: proteolysis;cell population proliferation;protein transport;cell migration;regulation of epidermal growth factor receptor signaling pathway;regulation of protein secretion;negative regulation of protein secretion;regulation of proteasomal protein catabolic process
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: serine-type endopeptidase activity;growth factor binding