RMND1

required for meiotic nuclear division 1 homolog

Basic information

Region (hg38): 6:151398898-151452158

Previous symbols: [ "C6orf96" ]

Links

ENSG00000155906 ∙ NCBI:55005 ∙ OMIM:614917 ∙ HGNC:21176 ∙ Uniprot:Q9NWS8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation defect type 11 (Strong), mode of inheritance: AR
• combined oxidative phosphorylation defect type 11 (Supportive), mode of inheritance: AR
• combined oxidative phosphorylation defect type 11 (Moderate), mode of inheritance: AR
• combined oxidative phosphorylation defect type 11 (Strong), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 11	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Cardiovascular; Musculoskeletal; Neurologic; Renal	18835491; 23022098; 23022099; 25058219

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RMND1 gene.

• not provided (11 variants)
• Combined oxidative phosphorylation defect type 11 (4 variants)
• Mitochondrial disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMND1 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			1	30	4	35
missense	1	2	60	3	5	71
nonsense	1					1
start loss						0
frameshift	11	5				16
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)		3	1			4
splice region			8	7		15
non coding			2	53	40	95
Total	13	10	66	87	49

Highest pathogenic variant AF is 0.0000197

Variants in RMND1

This is a list of pathogenic ClinVar variants found in the RMND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-151404858-C-CATTT			Benign (Jan 27, 2020)
6-151405040-G-T			Benign (Jun 23, 2018)
6-151405165-G-C			Benign (Jun 23, 2018)
6-151405236-C-G		Combined oxidative phosphorylation defect type 11 • Mitochondrial disease • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 17, 2024)
6-151405236-C-T		not specified	Benign (Jan 26, 2024)
6-151405237-A-G		Inborn genetic diseases	Likely pathogenic (Oct 26, 2017)
6-151405246-C-T			Likely benign (Nov 20, 2023)
6-151405248-C-T		Inborn genetic diseases	Uncertain significance (Sep 26, 2023)
6-151405250-T-C		not specified	Likely benign (Aug 02, 2017)
6-151405262-C-T			Uncertain significance (May 25, 2022)
6-151405264-T-G			Benign/Likely benign (Jun 12, 2023)
6-151405278-A-G		Combined oxidative phosphorylation defect type 11	Uncertain significance (Aug 19, 2022)
6-151405279-AAGTG-A			Likely benign (Sep 08, 2023)
6-151405621-T-C			Benign (Jun 23, 2018)
6-151405624-G-C			Likely benign (Jul 15, 2018)
6-151405662-GC-G			Likely benign (Jul 07, 2018)
6-151405694-C-T			Benign (Jun 23, 2018)
6-151405697-AGTAC-A			Likely benign (Oct 13, 2023)
6-151405699-TAC-T			Likely benign (Oct 24, 2023)
6-151405706-C-G			Likely benign (Oct 28, 2022)
6-151405708-T-C			Likely benign (Jul 17, 2022)
6-151405714-T-C			Uncertain significance (Jul 30, 2022)
6-151405717-T-G		Inborn genetic diseases	Uncertain significance (Aug 30, 2021)
6-151405719-C-A		Mitochondrial disease	Pathogenic (Dec 22, 2015)
6-151405734-G-A		Mitochondrial disease	Pathogenic (Dec 22, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMND1	protein_coding	protein_coding	ENST00000367303	11	47271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-9	0.526	125686	0	55	125741	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.765	201	234	0.859	0.0000116	2967
Missense in Polyphen		54	81.812	0.66005		1073
Synonymous	-0.0400	84	83.5	1.01	0.00000441	838
Loss of Function	1.17	17	23.0	0.738	0.00000115	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000566	0.000565
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000265	0.000264
Middle Eastern	0.000109	0.000109
South Asian	0.000168	0.000163
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for mitochondrial translation, possibly by coordinating the assembly or maintenance of the mitochondrial ribosome (PubMed:23022098, PubMed:25604853). {ECO:0000269|PubMed:23022098, ECO:0000269|PubMed:25604853}.
• Disease: DISEASE: Combined oxidative phosphorylation deficiency 11 (COXPD11) [MIM:614922]: A severe, multisystemic, autosomal recessive, disorder characterized by deficiencies of multiple mitochondrial respiratory enzymes leading to neonatal hypotonia and lactic acidosis. Affected individuals may have respiratory insufficiency, foot deformities, or seizures. {ECO:0000269|PubMed:23022098, ECO:0000269|PubMed:23022099, ECO:0000269|PubMed:25604853, ECO:0000269|PubMed:26238252}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.873
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.216
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmnd1

Gene ontology

• Biological process: translation;positive regulation of mitochondrial translation
• Cellular component: mitochondrion
• Molecular function: protein binding