LYRM7

LYR motif containing 7, the group of Mitochondrial respiratory chain complex assembly factors|LYR motif containing

Basic information

Region (hg38): 5:131170943-131205428

Previous symbols: [ "C5orf31" ]

Links

ENSG00000186687 ∙ NCBI:90624 ∙ OMIM:615831 ∙ HGNC:28072 ∙ Uniprot:Q5U5X0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex III deficiency nuclear type 8 (Strong), mode of inheritance: AR
• mitochondrial complex III deficiency (Supportive), 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
Mitochondrial complex III deficiency, nuclear type 8	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; Musculoskeletal; Neurologic	24014394

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LYRM7 gene.

• not provided (54 variants)
• Mitochondrial complex III deficiency nuclear type 8 (8 variants)
• not specified (5 variants)
• Inborn genetic diseases (3 variants)
• Mitochondrial complex III deficiency nuclear type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYRM7 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				3	1	4
missense		1	19	2		22
nonsense						0
start loss		1				1
frameshift	2	1				3
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region					2	2
non coding				18	12	30
Total	3	4	20	23	13

Highest pathogenic variant AF is 0.00000657

Variants in LYRM7

This is a list of pathogenic ClinVar variants found in the LYRM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-131170987-T-G		not specified	Likely benign (Aug 23, 2016)
5-131171005-C-T		not specified	Likely benign (Feb 09, 2016)
5-131171022-T-C		Mitochondrial complex III deficiency nuclear type 8	Conflicting classifications of pathogenicity (Jun 13, 2023)
5-131171025-G-A			Uncertain significance (Aug 22, 2022)
5-131171028-G-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
5-131171033-G-C		Inborn genetic diseases	Uncertain significance (Dec 15, 2022)
5-131171037-A-G			Uncertain significance (Mar 21, 2022)
5-131171038-G-C			Uncertain significance (Dec 02, 2021)
5-131171048-C-T		not specified	Benign (Jan 08, 2024)
5-131171052-G-A			Likely benign (May 03, 2021)
5-131171208-TTG-T			Benign (Jun 19, 2018)
5-131179944-A-T			Likely benign (Jun 29, 2018)
5-131180075-A-T			Likely benign (Nov 01, 2022)
5-131180095-GT-G			Pathogenic (Sep 09, 2022)
5-131180109-TA-T		Mitochondrial complex III deficiency nuclear type 8	Pathogenic (Dec 16, 2018)
5-131180118-G-A		not specified	Benign (Jan 29, 2024)
5-131180125-A-G			Uncertain significance (Aug 17, 2023)
5-131180127-C-T		LYRM7-related disorder	Likely benign (Jan 01, 2024)
5-131180149-G-A		Mitochondrial complex III deficiency nuclear type 8	Pathogenic (Dec 01, 2013)
5-131180152-G-A			Uncertain significance (Dec 11, 2023)
5-131180313-T-G			Benign (Jun 16, 2018)
5-131180382-C-CA			Benign (Aug 09, 2019)
5-131181953-C-G			Likely benign (Jun 28, 2018)
5-131182049-C-A			Benign (Jun 29, 2018)
5-131182077-A-G			Benign (Jun 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYRM7	protein_coding	protein_coding	ENST00000379380	5	34617

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0221	0.775	125546	0	3	125549	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	29	42.5	0.682	0.00000180	668
Missense in Polyphen		3	12.731	0.23564		225
Synonymous	-0.0358	15	14.8	1.01	6.36e-7	179
Loss of Function	0.915	3	5.26	0.570	2.22e-7	78

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Assembly factor required for Rieske Fe-S protein UQCRFS1 incorporation into the cytochrome b-c1 (CIII) complex. Functions as a chaperone, binding to this subunit within the mitochondrial matrix and stabilizing it prior to its translocation and insertion into the late CIII dimeric intermediate within the mitochondrial inner membrane. {ECO:0000269|PubMed:23168492}.
• Disease: DISEASE: Mitochondrial complex III deficiency, nuclear 8 (MC3DN8) [MIM:615838]: A form of mitochondrial complex III deficiency, a disorder of the mitochondrial respiratory chain resulting in a highly variable phenotype depending on which tissues are affected. Clinical features include mitochondrial encephalopathy, psychomotor retardation, ataxia, severe failure to thrive, liver dysfunction, renal tubulopathy, muscle weakness and exercise intolerance. {ECO:0000269|PubMed:24014394}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.613
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.0919
• hipred: N
• hipred_score: 0.240
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lyrm7

Gene ontology

• Biological process: mitochondrial respiratory chain complex III assembly;cellular respiration
• Cellular component: mitochondrial matrix;mitochondrial membrane
• Molecular function: protein binding