ATPSCKMT

protein-coding

ATP synthase c subunit lysine N-methyltransferase, the group of 7BS protein lysine methyltransferases

Gene summary

Enables protein-lysine N-methyltransferase activity. Involved in several processes, including peptidyl-lysine trimethylation; positive regulation of proton-transporting ATP synthase activity, rotational mechanism; and positive regulation of sensory perception of pain. Located in mitochondrial crista. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM173B

MANE transcript

NM_199133.4

Inheritance

—

ClinVar variants

U:42B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr5:10,225,507-10,249,897

External References & Databases

Ensembl (ENSG00000150756)

Transcript & Mutation Effects

hg38 • Region Span ~24.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATPSCKMT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199133.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			38 clinvar	1 clinvar		39
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	2	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199133.4	RefSeq	NP_954584.2	5	MANE Select
ENST00000511437.6	Ensembl	ENSP00000422338.1	5	MANE Select
NM_001258388.2	RefSeq	NP_001245317.1	4	Standard
NM_001258389.2	RefSeq	NP_001245318.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-lysine methylation
positive regulation of sensory perception of pain

Molecular Function

protein-lysine N-methyltransferase activity

Cellular Component

integral component of membrane
mitochondrial crista

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000511437
Coding exons: 5
Length: 23568
Individuals with no LoFs: 124664
Homozygous LoFs: 0
Heterozygous LoFs: 129
Defined: 124793
p: 0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.498	161	144	1.12	0.00000865	1491
Missense (PolyPhen)		58	58.355	0.99391		626
Synonymous	0.451	51	55.3	0.923	0.00000359	472
Loss of Function	-0.207	13	12.2	1.06	8.40e-7	113

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00078	0.00078	rare
Latino/Admixed American	0.00087	0.00087	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00078	0.00078	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00049	0.00049	rare
South Asian	0.00039	0.00039	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mitochondrial protein-lysine N-methyltransferase that promotes chronic pain (PubMed:29444090). Involved in persistent inflammatory and neuropathic pain: methyltransferase activity in the mitochondria of sensory neurons promotes chronic pain via a pathway that depends on the production of reactive oxygen species (ROS) and on the engagement of spinal cord microglia (PubMed:29444090). Protein-lysine N-methyltransferase activity is dependent on S-adenosyl-L-methionine (PubMed:29444090). Target proteins are unknown (PubMed:29444090). {ECO:0000269|PubMed:29444090}.;

Recessive Scores

pRec: 0.102

Intolerance Scores

LoFtool: 0.807
RVIS EVS: 0.42
RVIS percentile EVS: 77.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.797

Gene Damage Prediction

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