RHBDL3

rhomboid like 3, the group of EF-hand domain containing|Rhomboid family

Basic information

Region (hg38): 17:32265832-32324659

Previous symbols: [ "RHBDL4" ]

Links

ENSG00000141314 ∙ NCBI:162494 ∙ OMIM:619017 ∙ HGNC:16502 ∙ Uniprot:P58872 ∙ 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 RHBDL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDL3 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			21	1		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	21	1	0

Variants in RHBDL3

This is a list of pathogenic ClinVar variants found in the RHBDL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-32266281-T-C		not specified	Likely benign (Apr 07, 2023)
17-32266296-A-C		not specified	Uncertain significance (Oct 05, 2021)
17-32284779-G-A		not specified	Uncertain significance (Jun 29, 2023)
17-32288795-A-G		not specified	Uncertain significance (Jul 13, 2021)
17-32288805-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-32288819-C-G		not specified	Uncertain significance (Jun 05, 2023)
17-32288844-G-A		not specified	Uncertain significance (Oct 04, 2022)
17-32288846-A-T		not specified	Uncertain significance (Mar 31, 2024)
17-32288970-C-A		not specified	Uncertain significance (Mar 19, 2024)
17-32294328-G-A		not specified	Likely benign (May 26, 2024)
17-32305389-C-T		not specified	Uncertain significance (Jan 12, 2024)
17-32305412-G-A		not specified	Uncertain significance (Dec 20, 2023)
17-32305419-C-T		not specified	Uncertain significance (Feb 16, 2023)
17-32305428-C-A		not specified	Uncertain significance (Nov 17, 2022)
17-32316235-T-C		not specified	Uncertain significance (Dec 06, 2021)
17-32316261-G-T		not specified	Uncertain significance (Sep 25, 2023)
17-32320976-G-A		not specified	Uncertain significance (Jun 22, 2021)
17-32320990-C-T		not specified	Uncertain significance (Mar 16, 2024)
17-32320991-G-A		not specified	Uncertain significance (Jun 05, 2024)
17-32320996-C-T		not specified	Uncertain significance (Feb 10, 2022)
17-32321000-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-32321003-C-T		not specified	Uncertain significance (Aug 08, 2022)
17-32321033-T-C		not specified	Uncertain significance (Jul 11, 2023)
17-32321063-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-32321108-T-C		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RHBDL3	protein_coding	protein_coding	ENST00000269051	9	58486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.04e-7	0.783	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.627	208	235	0.885	0.0000144	2600
Missense in Polyphen		92	111.07	0.82834		1131
Synonymous	1.03	89	102	0.870	0.00000668	847
Loss of Function	1.40	14	20.9	0.669	0.00000116	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000388	0.000388
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in regulated intramembrane proteolysis and the subsequent release of functional polypeptides from their membrane anchors. {ECO:0000250}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.633
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.454
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0839

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rhbdl3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

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