ATP5MGL

ATP synthase membrane subunit g like

Basic information

Region (hg38): 22:42639803-42640601

Previous symbols: [ "ATP5K2", "ATP5L2" ]

Links

ENSG00000249222 ∙ NCBI:267020 ∙ ∙ HGNC:13213 ∙ Uniprot:Q7Z4Y8 ∙ 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 ATP5MGL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5MGL 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		1
missense			11	3		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	0

Variants in ATP5MGL

This is a list of pathogenic ClinVar variants found in the ATP5MGL region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42639975-G-C			Likely benign (Aug 01, 2023)
22-42639988-C-G		not specified	Uncertain significance (Nov 11, 2024)
22-42639988-C-T		not specified	Uncertain significance (Dec 03, 2021)
22-42640021-G-A		not specified	Likely benign (Sep 09, 2024)
22-42640058-C-T		not specified	Uncertain significance (Jan 08, 2024)
22-42640067-C-T		not specified	Uncertain significance (Jun 24, 2022)
22-42640106-C-A		not specified	Uncertain significance (Aug 21, 2024)
22-42640112-T-C		not specified	Uncertain significance (Aug 21, 2024)
22-42640136-G-A		not specified	Uncertain significance (Oct 14, 2023)
22-42640136-G-C		not specified	Uncertain significance (Oct 02, 2023)
22-42640172-T-C		not specified	Uncertain significance (Feb 16, 2023)
22-42640174-G-C		not specified	Likely benign (Sep 03, 2024)
22-42640190-C-T		not specified	Likely benign (Feb 21, 2024)
22-42640195-A-G		not specified	Uncertain significance (Dec 16, 2023)
22-42640196-A-T		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5MGL	protein_coding	protein_coding	ENST00000505920	1	799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000263	0.193	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.142	60	57.0	1.05	0.00000318	626
Missense in Polyphen		19	13.954	1.3617		204
Synonymous	-1.12	30	23.1	1.30	0.00000143	217
Loss of Function	-1.84	4	1.54	2.60	1.31e-7	14

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. Minor subunit located with subunit a in the membrane (By similarity). {ECO:0000250}.
• Pathway: adenosine ribonucleotides <i>de novo</i> biosynthesis;Purine metabolism;superpathway of purine nucleotide salvage;purine nucleotides <i>de novo</i> biosynthesis (Consensus)

Intolerance Scores

• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.94

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.421

Gene ontology

• Biological process: ATP synthesis coupled proton transport;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o);mitochondrion
• Molecular function: proton-transporting ATP synthase activity, rotational mechanism