UBE2A ubiquitin conjugating enzyme E2 A [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBE2Aprovided by HGNC
Official Full Name: ubiquitin conjugating enzyme E2 Aprovided by HGNC
Primary source: HGNC:HGNC:12472
See related: Ensembl:ENSG00000077721 MIM:312180; AllianceGenome:HGNC:12472
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: UBC2; HHR6A; MRXSN; RAD6A; MRXS30
Summary: The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin-protein ligases. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is required for post-replicative DNA damage repair, and may play a role in transcriptional regulation. Mutations in this gene are associated with cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Expression: Ubiquitous expression in placenta (RPKM 31.4), colon (RPKM 30.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xq24

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (119574563..119584423)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (117952276..117962139)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (118708526..118718386)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 in helix-3 affect ubiquitination activity and decrease enzyme stability.
Title: Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 in helix-3 affect ubiquitination activity and decrease enzyme stability.
Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.
Title: Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes.
A novel missense mutation in the UBE2A gene causes intellectual disability in the large X-linked family.
Title: A novel missense mutation in the UBE2A gene causes intellectual disability in the large X-linked family.
The Role of the Reanalysis of Genetic Test Results in the Diagnosis of Dysmorphic Syndrome Caused by Inherited xq24 Deletion including the UBE2A and CXorf56 Genes.
Title: The Role of the Reanalysis of Genetic Test Results in the Diagnosis of Dysmorphic Syndrome Caused by Inherited xq24 Deletion including the UBE2A and CXorf56 Genes.
A novel UBE2A mutation in a Chinese family with X-linked intellectual disability.
Title: A novel UBE2A mutation in a Chinese family with X-linked intellectual disability.
Refinement of the clinical and mutational spectrum of UBE2A deficiency syndrome.
Title: Refinement of the clinical and mutational spectrum of UBE2A deficiency syndrome.
Delineation of Clinical Manifestations of the Inherited Xq24 Microdeletion Segregating with sXCI in Mothers: Two Novel Cases with Distinct Phenotypes Ranging from UBE2A Deficiency Syndrome to Recurrent Pregnancy Loss.
Title: Delineation of Clinical Manifestations of the Inherited Xq24 Microdeletion Segregating with sXCI in Mothers: Two Novel Cases with Distinct Phenotypes Ranging from UBE2A Deficiency Syndrome to Recurrent Pregnancy Loss.
UBE2A mutations that are recurrently acquired during chronic myeloid leukemia progression interfere with myeloid differentiation pathways
Title: De novo UBE2A mutations are recurrently acquired during chronic myeloid leukemia progression and interfere with myeloid differentiation pathways.
These variants constitute the majority of the RAD6B transcriptome in contrast to RAD6A, which was predominantly wild-type. The expression of functional RAD6B variants only in melanomas reveals RAD6B's molecular heterogeneity and its association with melanoma pathogenesis.
Title: Alternative Splicing of RAD6B and Not RAD6A is Selectively Increased in Melanoma: Identification and Functional Characterization.
UBE2A Q93E mutation, which was identified in two brothers with mild intellectual disability, perturbs the UBE2A catalytic microenvironment essential for lysine deprotonation during ubiquitin transfer, thus generating an enzyme that is disabled but not dead.
Title: Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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

Associated conditions

Description	Tests
Syndromic X-linked intellectual disability Nascimento type MedGen: C3275464 OMIM: 300860 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-05-22) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2019-05-22) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity. 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

STS-M74524 (e-PCR)
- UniSTS:58149

A009F17 (e-PCR)
- UniSTS:62018

G32504 (e-PCR)
- UniSTS:117089

UBE2A_72 (e-PCR)
- UniSTS:276940

G44726 (e-PCR)
- UniSTS:95201

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin binding	TAS Traceable Author Statement more info
enables ubiquitin conjugating enzyme activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin conjugating enzyme activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA repair	IGI Inferred from Genetic Interaction more info	PubMed
involved_in G2/M transition of mitotic cell cycle	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of mitophagy	IDA Inferred from Direct Assay more info	PubMed
involved_in postreplication repair	NAS Non-traceable Author Statement more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein K11-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K48-linked ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	TAS Traceable Author Statement more info
involved_in response to UV	IGI Inferred from Genetic Interaction more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of HULC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HULC complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	TAS Traceable Author Statement more info
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: ubiquitin-conjugating enzyme E2 A

Names: E2 ubiquitin-conjugating enzyme A; RAD6 homolog A; ubiquitin carrier protein A; ubiquitin-conjugating enzyme E2A; ubiquitin-protein ligase A

NP_001269090.1

EC 2.3.2.23

NP_003327.2

EC 2.3.2.23

NP_861427.1

EC 2.3.2.23

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.

Genomic

NG_009267.1 RefSeqGene

Range

5028..14888

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001282161.2 → NP_001269090.1 ubiquitin-conjugating enzyme E2 A isoform 4

See identical proteins and their annotated locations for NP_001269090.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in its 5' UTR and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AI784380, DA068506, M74524

Consensus CDS

CCDS78500.1

UniProtKB/TrEMBL

A0A0D9SG71, B4DWT6

Related

ENSP00000487203.1, ENST00000628549.1

Conserved Domains (1) summary

pfam00179
Location:1 → 112

UQ_con; Ubiquitin-conjugating enzyme
NM_003336.4 → NP_003327.2 ubiquitin-conjugating enzyme E2 A isoform 1

See identical proteins and their annotated locations for NP_003327.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AI784380, DA599154, M74524

Consensus CDS

CCDS14580.1

UniProtKB/Swiss-Prot

A6NFE9, A6NGR2, A6NMF5, B2R7R9, D3DWI1, P49459, Q4TTG1, Q96FX4

UniProtKB/TrEMBL

Q53G86

Related

ENSP00000360613.2, ENST00000371558.7

Conserved Domains (1) summary

pfam00179
Location:8 → 145

UQ_con; Ubiquitin-conjugating enzyme
NM_181762.3 → NP_861427.1 ubiquitin-conjugating enzyme E2 A isoform 2

See identical proteins and their annotated locations for NP_861427.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AI784380, AK297696, DA599154, M74524

Consensus CDS

CCDS14581.1

UniProtKB/TrEMBL

Q53G86

Related

ENSP00000486599.1, ENST00000625938.2

Conserved Domains (1) summary

pfam00179
Location:8 → 115

UQ_con; Ubiquitin-conjugating enzyme

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_000023.11 Reference GRCh38.p14 Primary Assembly

Range

119574563..119584423

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GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

NW_025791817.1 Reference GRCh38.p14 PATCHES

Range

25564..35424

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

117952276..117962139

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_181777.1: Suppressed sequence

Description

NM_181777.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.