UBAC2 UBA domain containing 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBAC2provided by HGNC
Official Full Name: UBA domain containing 2provided by HGNC
Primary source: HGNC:HGNC:20486
See related: Ensembl:ENSG00000134882 AllianceGenome:HGNC:20486
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: PHGDHL1
Summary: Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 8.2), thyroid (RPKM 7.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q32.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (99200854..99386504)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (98411009..98596811)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (99853108..100038758)

Chromosome 13 - NC_000013.11 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: 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?

Association between UBAC2 gene polymorphism and the risk of noise-induced hearing loss: a cross-sectional study.
Title: Association between UBAC2 gene polymorphism and the risk of noise-induced hearing loss: a cross-sectional study.
UBAC2 promotes bladder cancer proliferation through BCRC-3/miRNA-182-5p/p27 axis.
Title: UBAC2 promotes bladder cancer proliferation through BCRC-3/miRNA-182-5p/p27 axis.
UBAC2 is associated with Behcet's disease in Chinese patients and implicates its involvement in transcriptional modulation.
Title: Replication study confirms the association between UBAC2 and Behçet's disease in two independent Chinese sets of patients and controls.
We established and confirmed the genetic association between UBAC2 and Behcet's disease in 3 independent sets of patients and controls
Title: A putative functional variant within the UBAC2 gene is associated with increased risk of Behçet's disease.
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 identifies novel alleles associated with risk of cutaneous basal cell carcinoma and squamous cell carcinoma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. 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

RH98849 (e-PCR)
- UniSTS:83713

D11S2921 (e-PCR)
- UniSTS:152074

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

WI-18855 (e-PCR)
- UniSTS:67407

L18426 (e-PCR)
- UniSTS:34648

G15934 (e-PCR)
- UniSTS:48235

SHGC-31753 (e-PCR)
- UniSTS:6795

GPR18_2306 (e-PCR)
- UniSTS:280715

WI-18159 (e-PCR)
- UniSTS:43147

GDB:451604 (e-PCR)
- UniSTS:157324

D11S3114 (e-PCR)
- UniSTS:152207

RH1615 (e-PCR)
- UniSTS:58003

SHGC-145779 (e-PCR)
- UniSTS:182694

PHGDHL1__5684 (e-PCR)
- UniSTS:463799

D14S792 (e-PCR)
- UniSTS:153529

EBI2_25 (e-PCR)
- UniSTS:277181

STS-AA011560 (e-PCR)
- UniSTS:70601

RH44801 (e-PCR)
- UniSTS:76235

L08177 (e-PCR)
- UniSTS:4047

RH11268 (e-PCR)
- UniSTS:43236

NoName (e-PCR)
- UniSTS:483565

Clone Names

FLJ26351, FLJ30001, FLJ30548, FLJ42413, MGC90487

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of canonical Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of retrograde protein transport, ER to cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ubiquitin-associated domain-containing protein 2

Names: RP11-178C10.1; UBA domain-containing protein 2; phosphoglycerate dehydrogenase like 1; phosphoglycerate dehydrogenase-like protein 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_001144072.2 → NP_001137544.1 ubiquitin-associated domain-containing protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_001137544.1

Status: VALIDATED

Description

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

Source sequence(s)

AI866141, AK075419, AK290342, AL136961, BC072674

Consensus CDS

CCDS45064.1

UniProtKB/Swiss-Prot

B3KNV7, Q0VAB5, Q5W0W6, Q5W0W9, Q6GQR2, Q6P4B0, Q8N2E8, Q8NBM4, Q96NW2

UniProtKB/TrEMBL

A8K2S7

Related

ENSP00000383911.3, ENST00000403766.8

Conserved Domains (1) summary

cd14305
Location:305 → 342

UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins
NM_177967.4 → NP_808882.1 ubiquitin-associated domain-containing protein 2 isoform 2

See identical proteins and their annotated locations for NP_808882.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' end exon and is missing two consecutive in-frame coding exons compared to transcript variant 1. This results in a shorter isoform (2) with a different N-terminus compares to isoform 1.

Source sequence(s)

AI866141, AK054563, AL136961, AL159981, BC072674

Consensus CDS

CCDS9490.1

UniProtKB/Swiss-Prot

Q8NBM4

Related

ENSP00000365623.2, ENST00000376440.6

Conserved Domains (1) summary

cd14305
Location:270 → 307

UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

RNA

NR_026644.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) contains an alternate 5' end exon compared to transcript variant 1, which results in use of downstream translation start site and premature translation termination, rendering this transcript susceptible to nonsense-mediated mRNA decay (NMD). This transcript is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.

Source sequence(s)

AI866141, AK054563, AL136961, AL159981, BC072674, BC121139

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

NC_000013.11 Reference GRCh38.p14 Primary Assembly

Range

99200854..99386504

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011521083.3 → XP_011519385.1 ubiquitin-associated domain-containing protein 2 isoform X2

Conserved Domains (1) summary

cd14305
Location:253 → 290

UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins
XM_011521082.3 → XP_011519384.2 ubiquitin-associated domain-containing protein 2 isoform X1
XM_047430286.1 → XP_047286242.1 ubiquitin-associated domain-containing protein 2 isoform X3

Related

ENST00000494576.5
XM_017020553.2 → XP_016876042.1 ubiquitin-associated domain-containing protein 2 isoform X4

Conserved Domains (1) summary

cd14305
Location:135 → 172

UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

NC_060937.1 Alternate T2T-CHM13v2.0

Range

98411009..98596811

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054374488.1 → XP_054230463.1 ubiquitin-associated domain-containing protein 2 isoform X2
XM_054374487.1 → XP_054230462.1 ubiquitin-associated domain-containing protein 2 isoform X1
XM_054374489.1 → XP_054230464.1 ubiquitin-associated domain-containing protein 2 isoform X3
XM_054374490.1 → XP_054230465.1 ubiquitin-associated domain-containing protein 2 isoform X4