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

Summary

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 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, Nov 2024]
Expression: Ubiquitous expression in fat (RPKM 4.0), adrenal (RPKM 3.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5p15.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (10225507..10249888, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (10164829..10189201, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (10225619..10250000, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-83804 (e-PCR)
- UniSTS:184260

WI-14366 (e-PCR)
- UniSTS:8928

SHGC-147960 (e-PCR)
- UniSTS:176124

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	IMP Inferred from Mutant Phenotype more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor more info
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
located_in mitochondrion	HTP 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

EC 2.1.1.-

NP_001245318.1

EC 2.1.1.-

NP_954584.2

EC 2.1.1.-

XP_011512266.1

EC 2.1.1.-

XP_047272669.1

EC 2.1.1.-

XP_054207586.1

EC 2.1.1.-

XP_054207587.1

EC 2.1.1.-

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)

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). ...
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). ...
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

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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

10225507..10249888 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060929.1 Alternate T2T-CHM13v2.0

Range

10164829..10189201 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054351611.1 → XP_054207586.1 ATP synthase subunit C lysine N-methyltransferase isoform X1
XM_054351612.1 → XP_054207587.1 ATP synthase subunit C lysine N-methyltransferase isoform X2