RHBDD3

rhomboid domain containing 3, the group of Rhomboid family

Basic information

Region (hg38): 22:29259872-29268209

Previous symbols: [ "C22orf3" ]

Links

ENSG00000100263 ∙ NCBI:25807 ∙ ∙ HGNC:1308 ∙ Uniprot:Q9Y3P4 ∙ 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 RHBDD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDD3 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			27	3		30
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	0

Variants in RHBDD3

This is a list of pathogenic ClinVar variants found in the RHBDD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-29260071-C-T		not specified	Uncertain significance (Mar 20, 2023)
22-29260109-G-T		not specified	Uncertain significance (May 03, 2023)
22-29260169-C-T		not specified	Uncertain significance (Feb 15, 2023)
22-29260196-G-A		not specified	Uncertain significance (Dec 27, 2023)
22-29260197-C-T		not specified	Uncertain significance (Jan 18, 2023)
22-29260229-T-G		not specified	Uncertain significance (Jan 05, 2022)
22-29260366-T-C		not specified	Uncertain significance (Apr 27, 2022)
22-29260477-C-T		not specified	Uncertain significance (May 23, 2023)
22-29260536-G-A		not specified	Uncertain significance (Mar 19, 2024)
22-29260543-G-C		not specified	Uncertain significance (Dec 11, 2023)
22-29260552-A-G		not specified	Uncertain significance (Dec 14, 2023)
22-29260590-T-A		not specified	Uncertain significance (Feb 03, 2022)
22-29260596-G-A		not specified	Uncertain significance (Aug 17, 2022)
22-29260611-G-A		not specified	Uncertain significance (Jun 07, 2024)
22-29260747-G-A		not specified	Uncertain significance (Aug 17, 2022)
22-29260780-G-A		not specified	Uncertain significance (Dec 26, 2023)
22-29260795-A-G		not specified	Uncertain significance (Sep 21, 2021)
22-29260799-C-T		not specified	Likely benign (Sep 12, 2023)
22-29260829-C-G		not specified	Uncertain significance (Sep 25, 2023)
22-29260846-C-T		not specified	Likely benign (Apr 04, 2023)
22-29260847-G-A		not specified	Uncertain significance (Nov 17, 2022)
22-29260856-C-G		not specified	Uncertain significance (Dec 11, 2023)
22-29263847-C-G		not specified	Uncertain significance (Sep 01, 2021)
22-29263909-A-G		not specified	Uncertain significance (Jul 21, 2021)
22-29263921-G-A		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHBDD3	protein_coding	protein_coding	ENST00000216085	5	8358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000495	0.680	123595	14	1906	125515	0.00768

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.102	197	201	0.980	0.0000120	2275
Missense in Polyphen		56	60.707	0.92247		801
Synonymous	0.373	95	99.7	0.952	0.00000622	917
Loss of Function	0.921	8	11.3	0.705	5.59e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00375	0.00364
Ashkenazi Jewish	0.00713	0.00697
East Asian	0.00	0.00
Finnish	0.0104	0.00995
European (Non-Finnish)	0.0134	0.0130
Middle Eastern	0.00	0.00
South Asian	0.000834	0.000784
Other	0.00894	0.00854

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0868

Intolerance Scores

• loftool: 0.703
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.06

Haploinsufficiency Scores

• pHI: 0.266
• hipred: N
• hipred_score: 0.146
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.710

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhbdd3
• Phenotype: homeostasis/metabolism phenotype; 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); liver/biliary system phenotype; immune system phenotype

Gene ontology

• Biological process: MAPK cascade;liver development;regulation of acute inflammatory response;proteolysis;response to xenobiotic stimulus;negative regulation of natural killer cell activation;positive regulation of protein catabolic process;regulation of protein secretion
• Cellular component: integral component of membrane
• Molecular function: serine-type endopeptidase activity