LYRM7

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

Basic information

Region (hg38): 5:131170944-131205428

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 (47 variants)
• Mitochondrial_complex_III_deficiency_nuclear_type_8 (14 variants)
• Inborn_genetic_diseases (7 variants)
• not_specified (3 variants)
• LYRM7-related_disorder (2 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. These statistics are base on transcript: NM_000181705.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	3		4
missense	1	1	23	2		27
nonsense	1					1
start loss		1				1
frameshift	3	1				4
splice donor/acceptor (+/-2bp)	1	1				2
Total	6	4	24	5	0

Highest pathogenic variant AF is 0.00000504001

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