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.

• not_specified (67 variants)
• not_provided (1 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_000012265.3. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			59	8		67
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	60	9	0

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