RHBDD1

rhomboid domain containing 1, the group of Rhomboid family

Basic information

Region (hg38): 2:226835581-226999215

Links

ENSG00000144468NCBI:84236OMIM:617515HGNC:23081Uniprot:Q8TEB9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RHBDD1 gene.

  • not_specified (41 variants)
  • not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001167608.3. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
41
clinvar
1
clinvar
42
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 41 1 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RHBDD1protein_codingprotein_codingENST00000392062 6163635
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.06e-120.01191257121301257430.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.02241711720.9950.000008712052
Missense in Polyphen3750.2730.73598601
Synonymous-0.4957064.91.080.00000358595
Loss of Function-0.5771714.61.166.16e-7181

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002750.000275
Ashkenazi Jewish0.000.00
East Asian0.0001650.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0001650.000163
South Asian0.0003270.000294
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Intramembrane-cleaving serine protease that cleaves single transmembrane or multi-pass membrane proteins in the hydrophobic plane of the membrane, luminal loops and juxtamembrane regions. Involved in regulated intramembrane proteolysis and the subsequent release of functional polypeptides from their membrane anchors. Functional component of endoplasmic reticulum-associated degradation (ERAD) for misfolded membrane proteins. Required for the degradation process of some specific misfolded endoplasmic reticulum (ER) luminal proteins. Participates in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner. Functions in BIK, MPZ, PKD1, PTCRA, RHO, STEAP3 and TRAC processing. Involved in the regulation of exosomal secretion; inhibits the TSAP6-mediated secretion pathway. Involved in the regulation of apoptosis; modulates BIK-mediated apoptotic activity. Also plays a role in the regulation of spermatogenesis; inhibits apoptotic activity in spermatogonia. {ECO:0000269|PubMed:18953687, ECO:0000269|PubMed:22624035}.;

Recessive Scores

pRec
0.0635

Intolerance Scores

loftool
0.966
rvis_EVS
0.77
rvis_percentile_EVS
87.06

Haploinsufficiency Scores

pHI
0.0430
hipred
N
hipred_score
0.167
ghis
0.443

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.436

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rhbdd1
Phenotype

Gene ontology

Biological process
apoptotic process;positive regulation of protein processing;membrane protein intracellular domain proteolysis;cellular response to unfolded protein;cellular response to UV;ERAD pathway;negative regulation of apoptotic process;post-translational protein modification;spermatid differentiation;positive regulation of secretion;membrane protein proteolysis involved in retrograde protein transport, ER to cytosol;regulation of male germ cell proliferation
Cellular component
mitochondrion;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of endoplasmic reticulum membrane;endoplasmic reticulum quality control compartment
Molecular function
endopeptidase activity;serine-type endopeptidase activity