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.

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.

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	5	8
missense			62	2	2	66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	5	7

Variants in RHBDF1

This is a list of pathogenic ClinVar variants found in the RHBDF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-58426-G-A		not specified	Uncertain significance (Jun 12, 2023)
16-58455-A-G		not specified	Uncertain significance (Dec 15, 2022)
16-58513-G-A		not specified	Uncertain significance (Apr 04, 2023)
16-58526-C-G		not specified	Uncertain significance (Jun 22, 2023)
16-58642-G-T			Likely benign (Mar 01, 2023)
16-58735-C-G		not specified	Uncertain significance (Dec 17, 2023)
16-59015-C-T		not specified	Uncertain significance (Nov 17, 2023)
16-59050-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-59290-G-A			Benign (May 18, 2018)
16-59313-A-G		not specified	Uncertain significance (Dec 19, 2022)
16-59477-C-T		not specified	Uncertain significance (Sep 26, 2022)
16-59478-G-A		not specified	Uncertain significance (Dec 28, 2022)
16-59759-C-T		not specified	Uncertain significance (May 31, 2023)
16-59776-G-A			Likely benign (Jul 01, 2022)
16-60236-C-G		not specified	Uncertain significance (Jan 03, 2024)
16-60238-G-A		not specified	Uncertain significance (Aug 28, 2023)
16-60265-G-A		not specified	Uncertain significance (Feb 26, 2024)
16-60469-T-C		not specified	Uncertain significance (Mar 14, 2023)
16-60484-G-A		Wolff-Parkinson-White pattern	Uncertain significance (Jul 14, 2017)
16-60494-G-A		not specified	Uncertain significance (Mar 28, 2024)
16-60503-G-A		not specified	Uncertain significance (Jan 19, 2024)
16-60511-G-A		not specified	Uncertain significance (Sep 20, 2023)
16-61128-C-G		not specified	Uncertain significance (Aug 28, 2023)
16-61130-T-C		not specified	Uncertain significance (Oct 13, 2023)
16-61159-G-C		not specified	Uncertain significance (Oct 12, 2021)

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
5.41e-15	0.769	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

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.697
• ghis: 0.620

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

Mouse Genome Informatics

• Gene name: Rhbdf1
• Phenotype: immune system phenotype; skeleton phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

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