RHBDL2

rhomboid like 2, the group of Rhomboid family

Basic information

Region (hg38): 1:38885806-38941830

Links

ENSG00000158315 ∙ NCBI:54933 ∙ OMIM:608962 ∙ HGNC:16083 ∙ Uniprot:Q9NX52 ∙ 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 RHBDL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDL2 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						0
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in RHBDL2

This is a list of pathogenic ClinVar variants found in the RHBDL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-38886523-A-G		not specified	Uncertain significance (Jan 31, 2024)
1-38886562-T-G		not specified	Uncertain significance (Mar 01, 2023)
1-38886665-T-C		not specified	Likely benign (Jan 22, 2024)
1-38887979-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-38895992-C-G		not specified	Uncertain significance (Jun 18, 2024)
1-38896036-C-G		not specified	Uncertain significance (Aug 08, 2023)
1-38911357-C-T		not specified	Uncertain significance (Jun 04, 2024)
1-38911358-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-38911396-A-G		not specified	Uncertain significance (Mar 29, 2022)
1-38915625-A-C		not specified	Uncertain significance (Nov 21, 2022)
1-38915632-G-A		not specified	Uncertain significance (Apr 27, 2023)
1-38915647-C-T		not specified	Uncertain significance (Apr 13, 2022)
1-38915656-A-T		not specified	Uncertain significance (Jan 10, 2022)
1-38915707-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-38919047-C-T		not specified	Uncertain significance (Oct 30, 2023)
1-38919130-T-G		not specified	Uncertain significance (Jan 19, 2022)
1-38919144-C-A		not specified	Uncertain significance (Nov 17, 2022)
1-38919188-T-A		not specified	Uncertain significance (Mar 29, 2022)
1-38919199-T-C		not specified	Uncertain significance (Jul 25, 2023)
1-38919202-A-G		not specified	Likely benign (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHBDL2	protein_coding	protein_coding	ENST00000289248	7	55993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.94e-8	0.311	125483	0	262	125745	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0707	159	162	0.984	0.00000783	1991
Missense in Polyphen		39	47.562	0.81999		585
Synonymous	1.41	45	58.8	0.766	0.00000304	577
Loss of Function	0.539	12	14.2	0.846	6.83e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00175	0.00175
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000743	0.000739
European (Non-Finnish)	0.00163	0.00162
Middle Eastern	0.000109	0.000109
South Asian	0.0000994	0.0000980
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulated intramembrane proteolysis and the subsequent release of functional polypeptides from their membrane anchors. Known substrate: EFNB3. {ECO:0000269|PubMed:11672525, ECO:0000269|PubMed:15047175}.
• Pathway: DroToll-like (Consensus)

Recessive Scores

• pRec: 0.0856

Intolerance Scores

• loftool: 0.812
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.0744
• hipred: N
• hipred_score: 0.377
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rhbdl2

Gene ontology

• Biological process: proteolysis
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: serine-type endopeptidase activity