ATPSCKMT

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

Basic information

Region (hg38): 5:10225506-10249897

Previous symbols: [ "FAM173B" ]

Links

ENSG00000150756 ∙ NCBI:134145 ∙ OMIM:618568 ∙ HGNC:27029 ∙ Uniprot:Q6P4H8 ∙ 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 ATPSCKMT gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

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

Variants in ATPSCKMT

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

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

Position	Type	Phenotype	Significance	ClinVar
5-10227466-T-G		not specified	Uncertain significance (Jul 12, 2023)
5-10227472-G-A		not specified	Uncertain significance (Dec 19, 2022)
5-10227472-G-C		not specified	Uncertain significance (Aug 16, 2021)
5-10227514-T-C		not specified	Uncertain significance (Jan 10, 2023)
5-10227564-C-A		not specified	Uncertain significance (Mar 07, 2024)
5-10227599-G-A			Likely benign (Mar 01, 2023)
5-10236536-C-T		not specified	Uncertain significance (Dec 15, 2022)
5-10236572-T-A		not specified	Uncertain significance (Jul 12, 2022)
5-10239116-C-T		not specified	Likely benign (Oct 06, 2021)
5-10239159-G-A		not specified	Uncertain significance (Dec 17, 2021)
5-10239194-G-A		not specified	Uncertain significance (Oct 13, 2023)
5-10239203-G-A		not specified	Uncertain significance (Apr 28, 2022)
5-10239312-C-A		not specified	Uncertain significance (Sep 14, 2022)
5-10239312-C-T		not specified	Uncertain significance (Aug 28, 2023)
5-10239327-T-C		not specified	Uncertain significance (Dec 02, 2021)
5-10249898-A-T			Benign (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATPSCKMT	protein_coding	protein_coding	ENST00000511437	5	23568

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.78e-9	0.0675	124664	0	129	124793	0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.498	161	144	1.12	0.00000865	1491
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00164	0.00164
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000779	0.000779
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000487	0.000486
Middle Eastern	0.000779	0.000779
South Asian	0.000392	0.000392
Other	0.000165	0.000165

dbNSFP

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

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam173b

Gene ontology

• Biological process: peptidyl-lysine methylation;positive regulation of sensory perception of pain
• Cellular component: integral component of membrane;mitochondrial crista
• Molecular function: protein-lysine N-methyltransferase activity