RHBDD2

rhomboid domain containing 2, the group of Rhomboid family

Basic information

Region (hg38): 7:75842602-75888926

Previous symbols: [ "RHBDL7" ]

Links

ENSG00000005486 ∙ NCBI:57414 ∙ OMIM:615203 ∙ HGNC:23082 ∙ Uniprot:Q6NTF9 ∙ 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 RHBDD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDD2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in RHBDD2

This is a list of pathogenic ClinVar variants found in the RHBDD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-75879089-G-A		not specified	Uncertain significance (Sep 14, 2022)
7-75879098-C-T		not specified	Uncertain significance (Aug 17, 2022)
7-75879118-C-G		not specified	Uncertain significance (May 25, 2022)
7-75879131-G-A		not specified	Uncertain significance (Aug 04, 2023)
7-75879146-T-A		not specified	Uncertain significance (Jan 12, 2024)
7-75881898-T-C		not specified	Uncertain significance (Dec 15, 2023)
7-75881903-C-T		not specified	Uncertain significance (Nov 05, 2021)
7-75881904-G-A			Uncertain significance (Apr 05, 2013)
7-75881985-T-C		not specified	Uncertain significance (Jun 18, 2024)
7-75882011-T-C		not specified	Uncertain significance (Mar 29, 2023)
7-75882092-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-75882095-C-A		not specified	Uncertain significance (Sep 29, 2023)
7-75882171-C-T		not specified	Uncertain significance (May 26, 2024)
7-75882192-C-T		not specified	Uncertain significance (Mar 01, 2024)
7-75882233-G-A		not specified	Uncertain significance (Jun 07, 2024)
7-75883724-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-75883743-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-75883750-G-T		not specified	Uncertain significance (Dec 13, 2023)
7-75883765-C-G		not specified	Uncertain significance (Oct 03, 2022)
7-75883836-C-T		not specified	Uncertain significance (Jun 09, 2022)
7-75888012-C-T		not specified	Uncertain significance (Jul 14, 2023)
7-75888074-C-G		not specified	Uncertain significance (Feb 07, 2023)
7-75888126-T-C		not specified	Uncertain significance (Jul 25, 2023)
7-75888191-A-G		not specified	Uncertain significance (Jun 12, 2023)
7-75888213-A-C		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHBDD2	protein_coding	protein_coding	ENST00000006777	4	46325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.639	0.360	124808	0	5	124813	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.665	183	210	0.871	0.0000127	2281
Missense in Polyphen		58	71.628	0.80973		731
Synonymous	0.724	91	100	0.908	0.00000678	832
Loss of Function	2.66	2	11.9	0.168	5.94e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.00000888	0.00000882
Middle Eastern	0.000111	0.000111
South Asian	0.0000329	0.0000327
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0462
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.283
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.433

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhbdd2

Gene ontology

• Biological process: proteolysis
• Cellular component: Golgi membrane;nucleus;nucleoplasm;Golgi apparatus;integral component of membrane;perinuclear region of cytoplasm
• Molecular function: serine-type endopeptidase activity