RMND5B

required for meiotic nuclear division 5 homolog B

Basic information

Region (hg38): 5:178130995-178150568

Links

ENSG00000145916 ∙ NCBI:64777 ∙ ∙ HGNC:26181 ∙ Uniprot:Q96G75 ∙ 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 RMND5B gene.

• Dyskeratosis congenita (31 variants)
• Inborn genetic diseases (15 variants)
• not provided (8 variants)
• not specified (4 variants)
• Dyskeratosis congenita, autosomal recessive 2 (2 variants)
• Dyskeratosis congenita, autosomal recessive 2;Dyskeratosis congenita, autosomal recessive 1 (1 variants)
• Dyskeratosis congenita, autosomal recessive 1 (1 variants)
• Dyskeratosis congenita, autosomal recessive 1;Dyskeratosis congenita, autosomal recessive 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMND5B 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1		21	15	1	38
Total	1	0	36	15	1

Variants in RMND5B

This is a list of pathogenic ClinVar variants found in the RMND5B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-178138207-G-C		not specified	Uncertain significance (Nov 09, 2023)
5-178138219-C-T		not specified	Uncertain significance (Jan 05, 2022)
5-178138238-G-A		not specified	Uncertain significance (Apr 25, 2022)
5-178142595-C-A		not specified	Uncertain significance (Oct 14, 2023)
5-178142639-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-178142870-T-C		not specified	Uncertain significance (May 03, 2023)
5-178142874-G-A		not specified	Uncertain significance (Dec 28, 2022)
5-178142901-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-178142936-A-G		not specified	Uncertain significance (Dec 11, 2023)
5-178142972-G-A		not specified	Uncertain significance (Oct 26, 2022)
5-178143949-G-A		not specified	Uncertain significance (Feb 13, 2023)
5-178146140-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-178146195-G-A		not specified	Uncertain significance (Feb 05, 2024)
5-178146212-T-C		not specified	Uncertain significance (Nov 13, 2023)
5-178146227-C-T		not specified	Uncertain significance (Nov 12, 2021)
5-178146228-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-178147593-G-T		not specified	Uncertain significance (Dec 06, 2022)
5-178147615-A-G		not specified	Uncertain significance (Feb 17, 2024)
5-178147621-A-G		not specified	Uncertain significance (Nov 18, 2022)
5-178147634-C-T		not specified	Uncertain significance (May 25, 2022)
5-178147736-T-C		not specified	Uncertain significance (Mar 15, 2023)
5-178147799-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-178147808-C-G		not specified	Uncertain significance (Dec 17, 2023)
5-178147828-A-G		not specified	Uncertain significance (Oct 20, 2023)
5-178149487-C-T			Likely benign (Feb 13, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMND5B	protein_coding	protein_coding	ENST00000515098	9	19570

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.95e-13	0.0595	125597	1	150	125748	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.706	212	243	0.873	0.0000151	2554
Missense in Polyphen		53	67.608	0.78393		764
Synonymous	0.135	103	105	0.983	0.00000673	779
Loss of Function	0.467	21	23.4	0.896	0.00000129	240

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000695	0.000695
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000278	0.000277
European (Non-Finnish)	0.00102	0.00101
Middle Eastern	0.000272	0.000272
South Asian	0.000262	0.000261
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1. MAEA and RMND5A are both required for catalytic activity of the CTLH E3 ubiquitin-protein ligase complex (PubMed:29911972). Catalytic activity of the complex is required for normal cell proliferation (PubMed:29911972). The CTLH E3 ubiquitin-protein ligase complex is not required for the degradation of enzymes involved in gluconeogenesis, such as FBP1 (PubMed:29911972). {ECO:0000269|PubMed:29911972}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.389
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmnd5b

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: nucleus;cytoplasm;cytosol;GID complex
• Molecular function: ubiquitin-protein transferase activity;metal ion binding