RMND5A

required for meiotic nuclear division 5 homolog A, the group of CTLH complex

Basic information

Region (hg38): 2:86720291-86778041

Links

ENSG00000153561 ∙ NCBI:64795 ∙ OMIM:618964 ∙ HGNC:25850 ∙ Uniprot:Q9H871 ∙ 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 RMND5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMND5A 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in RMND5A

This is a list of pathogenic ClinVar variants found in the RMND5A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86720731-G-C		not specified	Uncertain significance (Feb 27, 2023)
2-86740947-G-C		not specified	Uncertain significance (Jul 12, 2022)
2-86741016-G-A		not specified	Uncertain significance (Nov 22, 2023)
2-86741052-G-A		not specified	Uncertain significance (Mar 07, 2023)
2-86753548-C-G		not specified	Uncertain significance (Jun 13, 2022)
2-86765955-T-C		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMND5A	protein_coding	protein_coding	ENST00000283632	9	57869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.900	0.100	125738	0	7	125745	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	95	202	0.471	0.00000951	2556
Missense in Polyphen		13	51.187	0.25397		666
Synonymous	-0.313	77	73.6	1.05	0.00000346	709
Loss of Function	3.60	3	20.6	0.145	9.37e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000110	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.0886

Intolerance Scores

• loftool: 0.150
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.349
• hipred: Y
• hipred_score: 0.825
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.213

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmnd5a

Gene ontology

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