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ATPSCKMT ATP synthase c subunit lysine N-methyltransferase [ Homo sapiens (human) ]

Gene ID: 134145, updated on 30-Mar-2024

Summary

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Official Symbol
ATPSCKMTprovided by HGNC
Official Full Name
ATP synthase c subunit lysine N-methyltransferaseprovided by HGNC
Primary source
HGNC:HGNC:27029
See related
Ensembl:ENSG00000150756 MIM:618568; AllianceGenome:HGNC:27029
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
JS-2; FAM173B; hFAM173B
Summary
Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation; positive regulation of sensory perception of pain; and regulation of proton transport. Located in mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 4.0), adrenal (RPKM 3.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5p15.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (10225507..10249888, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (10164829..10189201, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (10225619..10250000, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986405 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944391-9944892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:9944893-9945392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15911 Neighboring gene uncharacterized LOC124900939 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10101715-10102617 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10102618-10103520 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:10108167-10108948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:10127135-10127785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10140102-10140735 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:10157229-10157880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15915 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15916 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10251320-10251542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22352 Neighboring gene chaperonin containing TCP1 subunit 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:10300268-10300444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:10307292-10307792 Neighboring gene carboxymethylenebutenolidase homolog

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Altered JS-2 expression in colorectal cancers and its clinical pathological relevance. Lam AK, et al. Mol Oncol, 2011 Oct. PMID 21802380, Free PMC Article
  2. Expression of mitochondrial TSPO and FAM173B is associated with inflammation and symptoms in patients with painful knee osteoarthritis. Palada V, et al. Rheumatology (Oxford), 2021 Apr 6. PMID 33067627, Free PMC Article
  3. Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region. Peters MJ, et al. Ann Rheum Dis, 2013 Mar. PMID 22956598, Free PMC Article
  4. Transforming capacity of two novel genes JS-1 and JS-2 located in chromosome 5p and their overexpression in human esophageal squamous cell carcinoma. Fatima S, et al. Int J Mol Med, 2006 Jan. PMID 16328025
  5. Identification of FAM173B as a protein methyltransferase promoting chronic pain. Willemen HLDM, et al. PLoS Biol, 2018 Feb. PMID 29444090, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression of mitochondrial TSPO and FAM173B is associated with inflammation and symptoms in patients with painful knee osteoarthritis.
    Title: Expression of mitochondrial TSPO and FAM173B is associated with inflammation and symptoms in patients with painful knee osteoarthritis.
  2. It has been identified FAM173B as the long-sought KMT responsible for methylation of ATP synthase c-subunit (ATPSc), a key protein in cellular ATP production, and have demonstrated functional significance of ATPSc methylation.
    Title: Lysine methylation by the mitochondrial methyltransferase FAM173B optimizes the function of mitochondrial ATP synthase.
  3. we uncover a role for methyltransferase activity of FAM173B in the neurobiology of pain. These results also highlight FAM173B methyltransferase activity as a potential therapeutic target to treat debilitating chronic pain conditions
    Title: Identification of FAM173B as a protein methyltransferase promoting chronic pain.
  4. Genetic alteration of JS-2 was found to be related to location, pathological subtypes and staging of colorectal cancer.
    Title: Altered JS-2 expression in colorectal cancers and its clinical pathological relevance.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study meta-analysis of chronic widespread pain: evidence for involvement of the 5p15.2 region.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20667

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables histone methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-lysine N-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein-lysine N-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein-lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in peptidyl-lysine methylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in peptidyl-lysine trimethylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-lysine trimethylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of proton-transporting ATP synthase activity, rotational mechanism IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of proton-transporting ATP synthase activity, rotational mechanism IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of mitochondrial ATP synthesis coupled proton transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of mitochondrial ATP synthesis coupled proton transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in mitochondrial crista IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ATP synthase subunit C lysine N-methyltransferase
Names
family with sequence similarity 173 member B
protein FAM173B
protein N-lysine methyltransferase FAM173B
NP_001245317.1
NP_001245318.1
NP_954584.2
XP_011512266.1
XP_047272669.1
XP_054207586.1
XP_054207587.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001258388.2 → NP_001245317.1  ATP synthase subunit C lysine N-methyltransferase isoform 2

    See identical proteins and their annotated locations for NP_001245317.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC034229, AK302012, DW420473
    Consensus CDS
    CCDS58942.1
    UniProtKB/TrEMBL
    B7ZAK2
    Related
    ENSP00000420876.1, ENST00000510047.5
    Conserved Domains (1) summary
    cl17173
    Location:83 → 190
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  2. NM_001258389.2 → NP_001245318.1  ATP synthase subunit C lysine N-methyltransferase isoform 3

    See identical proteins and their annotated locations for NP_001245318.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (3) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC034229, DA523490
    Conserved Domains (1) summary
    cl17173
    Location:88 → 123
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

  3. NM_199133.4 → NP_954584.2  ATP synthase subunit C lysine N-methyltransferase isoform 1

    See identical proteins and their annotated locations for NP_954584.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC034229, AK300042, GD160552
    Consensus CDS
    CCDS43301.1
    UniProtKB/Swiss-Prot
    B4DT41, B4DXK2, E9PBZ4, Q6P4H8
    UniProtKB/TrEMBL
    B7ZAK2
    Related
    ENSP00000422338.1, ENST00000511437.6
    Conserved Domains (1) summary
    cl17173
    Location:83 → 188
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

RNA

  1. NR_047668.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC034229, DA843869, DW420473

  2. NR_047669.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC034229, BG611454

  3. NR_047670.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) contains an alternate internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC034229, AK055604

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    10225507..10249888 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416713.1 → XP_047272669.1  ATP synthase subunit C lysine N-methyltransferase isoform X1

  2. XM_011513964.2 → XP_011512266.1  ATP synthase subunit C lysine N-methyltransferase isoform X2

    Conserved Domains (1) summary
    cl17173
    Location:83 → 176
    AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    10164829..10189201 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351611.1 → XP_054207586.1  ATP synthase subunit C lysine N-methyltransferase isoform X1

  2. XM_054351612.1 → XP_054207587.1  ATP synthase subunit C lysine N-methyltransferase isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P4H8.2 GenPept UniProtKB/Swiss-Prot:Q6P4H8

Gene LinkOut

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