ATP5MK

ATP synthase membrane subunit k, the group of Mitochondrial complex V: ATP synthase subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:103389041-103396492

Previous symbols: [ "USMG5", "ATP5MD" ]

Links

ENSG00000173915 ∙ NCBI:84833 ∙ OMIM:615204 ∙ HGNC:30889 ∙ Uniprot:Q96IX5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leigh syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex V (ATP synthase) deficiency, nuclear type 6	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; Neurologic	29917077

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5MK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5MK 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	1	5	0	0

Variants in ATP5MK

This is a list of pathogenic ClinVar variants found in the ATP5MK region.

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

Position	Type	Phenotype	Significance	ClinVar
10-103392230-T-G		not specified	Uncertain significance (Apr 29, 2024)
10-103392258-A-G		not specified	Uncertain significance (Apr 13, 2022)
10-103392368-T-TA		Mitochondrial complex 5 (ATP synthase) deficiency, nuclear type 6	Likely pathogenic (Sep 22, 2020)
10-103392370-C-G		Mitochondrial complex 5 (ATP synthase) deficiency, nuclear type 6	Pathogenic (Dec 02, 2019)
10-103392390-G-A		not specified	Uncertain significance (Oct 02, 2023)
10-103392399-T-C		Mitochondrial complex 5 (ATP synthase) deficiency, nuclear type 6	Uncertain significance (Jun 03, 2020)
10-103392435-G-A		not specified	Uncertain significance (Jul 20, 2021)
10-103392445-C-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5MK	protein_coding	protein_coding	ENST00000369825	2	7426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0480	0.698	125488	0	54	125542	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0855	27	28.3	0.955	0.00000128	367
Missense in Polyphen		3	4.2652	0.70337		57
Synonymous	-1.16	16	11.1	1.44	5.54e-7	112
Loss of Function	0.628	2	3.21	0.622	2.27e-7	39

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00344	0.00328
East Asian	0.000654	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.0000633	0.0000616
Middle Eastern	0.000654	0.000653
South Asian	0.00	0.00
Other	0.000341	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in maintaining the ATP synthase population in mitochondria. {ECO:0000269|PubMed:21345788}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.767
• ghis: 0.416

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Usmg5
• Phenotype: hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: atp5md
• Affected structure: atrium
• Phenotype tag: abnormal
• Phenotype quality: increased area

Gene ontology

• Cellular component: mitochondrion;mitochondrial proton-transporting ATP synthase complex;integral component of membrane