HERPUD1 homocysteine inducible ER protein with ubiquitin like domain 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HERPUD1provided by HGNC
Official Full Name: homocysteine inducible ER protein with ubiquitin like domain 1provided by HGNC
Primary source: HGNC:HGNC:13744
See related: Ensembl:ENSG00000051108 MIM:608070; AllianceGenome:HGNC:13744
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: SUP; HERP; Mif1
Summary: The accumulation of unfolded proteins in the endoplasmic reticulum (ER) triggers the ER stress response. This response includes the inhibition of translation to prevent further accumulation of unfolded proteins, the increased expression of proteins involved in polypeptide folding, known as the unfolded protein response (UPR), and the destruction of misfolded proteins by the ER-associated protein degradation (ERAD) system. This gene may play a role in both UPR and ERAD. Its expression is induced by UPR and it has an ER stress response element in its promoter region while the encoded protein has an N-terminal ubiquitin-like domain which may interact with the ERAD system. This protein has been shown to interact with presenilin proteins and to increase the level of amyloid-beta protein following its overexpression. Alternative splicing of this gene produces multiple transcript variants encoding different isoforms. The full-length nature of all transcript variants has not been determined. [provided by RefSeq, Jan 2013]
Expression: Ubiquitous expression in thyroid (RPKM 145.7), prostate (RPKM 120.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q13

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (56932142..56944864)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (62728473..62741195)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (56966054..56978776)

Chromosome 16 - NC_000016.10 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 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?

Herpud1 deficiency alleviates homocysteine-induced aortic valve calcification.
Title: Herpud1 deficiency alleviates homocysteine-induced aortic valve calcification.
Association of HERPUD1 genetic variant rs2217332 with age-related macular degeneration and polypoidal choroidal vasculopathy in an Indian cohort.
Title: Association of HERPUD1 genetic variant rs2217332 with age-related macular degeneration and polypoidal choroidal vasculopathy in an Indian cohort.
HERPUD1 promotes ovarian cancer cell survival by sustaining autophagy and inhibit apoptosis via PI3K/AKT/mTOR and p38 MAPK signaling pathways.
Title: HERPUD1 promotes ovarian cancer cell survival by sustaining autophagy and inhibit apoptosis via PI3K/AKT/mTOR and p38 MAPK signaling pathways.
The Brucella effector BspL targets the ER-associated degradation (ERAD) pathway and delays bacterial egress from infected cells.
Title: The Brucella effector BspL targets the ER-associated degradation (ERAD) pathway and delays bacterial egress from infected cells.
Herpud1 deficiency could reduce amyloid-beta40 expression and thereby suppress homocysteine-induced atherosclerosis by blocking the JNK/AP1 pathway.
Title: Herpud1 deficiency could reduce amyloid-β40 expression and thereby suppress homocysteine-induced atherosclerosis by blocking the JNK/AP1 pathway.
The cytosolic relocalization of endoplasmic reticulum chaperone BiP did not require the function of translocon and was counteracted by HERP, a component of endoplasmic reticulum-associated protein degradation.
Title: The endoplasmic reticulum-residing chaperone BiP is short-lived and metabolized through N-terminal arginylation.
This study showed that Herp stability was regulated by synoviolin through lysine ubiquitination-independent proteasomal degradation.
Title: An E3 Ubiquitin Ligase, Synoviolin, Is Involved in the Degradation of Homocysteine-Inducible Endoplasmic Reticulum Protein.
HERP plays an important role in the regulation of host innate immunity in response to ER stress during the infection of RNA viruses.
Title: HERP Binds TBK1 To Activate Innate Immunity and Repress Virus Replication in Response to Endoplasmic Reticulum Stress.
results indicated that low expression of miR-9-3p results in a high level of Herpud1, which may protect against apoptosis in glioma
Title: MiR-9-3p augments apoptosis induced by H2O2 through down regulation of Herpud1 in glioma.
Thus, our findings indicated that NQO1 could stabilize Herp protein expression via indirect regulation of synoviolin.
Title: NAD(P)H quinone oxidoreductase 1 inhibits the proteasomal degradation of homocysteine-induced endoplasmic reticulum protein.

Submit: New GeneRIF Correction See all GeneRIFs (32)

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
A genome-wide association study of the metabolic syndrome in Indian Asian men. EBI GWAS Catalog EBI GWAS CatalogPubMed
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study. EBI GWAS Catalog EBI GWAS CatalogPubMed
Polymorphism in the CETP gene region, HDL cholesterol, and risk of future myocardial infarction: Genomewide analysis among 18 245 initially healthy women from the Women's Genome Health Study. 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

D16S3200 (e-PCR)
- UniSTS:76071

RH25263 (e-PCR)
- UniSTS:89571

SHGC-61031 (e-PCR)
- UniSTS:6122

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane transporter binding	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin-like ligase-substrate adaptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum calcium ion homeostasis	IDA Inferred from Direct Assay more info	PubMed
involved_in endoplasmic reticulum unfolded protein response	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of intrinsic apoptotic signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of ERAD pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in protein targeting to ER	IEA Inferred from Electronic Annotation more info
involved_in regulation of ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in response to endoplasmic reticulum stress	TAS Traceable Author Statement more info	PubMed
involved_in response to unfolded protein	IEP Inferred from Expression Pattern more info	PubMed
involved_in retrograde protein transport, ER to cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Lewy body core	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum quality control compartment	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed

General protein information

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Preferred Names: homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein

Names: MMS-inducible; homocysteine-inducible endoplasmic reticulum stress-inducible ubiquitin-like domain member 1 protein; homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1; methyl methanesulfonate (MMF)-inducible fragment 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_001010989.3 → NP_001010989.1 homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein isoform 2

See identical proteins and their annotated locations for NP_001010989.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2).

Source sequence(s)

AC012181, AF055003, DA581153

Consensus CDS

CCDS45492.1

UniProtKB/TrEMBL

A0A2Z2EHH6, A8K6A0, A8K7S3, Q53FP9

Related

ENSP00000300302.5, ENST00000300302.9

Conserved Domains (1) summary

cd17118
Location:9 → 85

Ubl_HERP1; ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins
NM_001272103.2 → NP_001259032.1 homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein isoform 4

See identical proteins and their annotated locations for NP_001259032.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC012181, AF055001, DA581153, DQ837586

UniProtKB/TrEMBL

A4UAE9

Conserved Domains (1) summary

cd17118
Location:9 → 86

Ubl_HERP1; ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins
NM_014685.4 → NP_055500.1 homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein isoform 1

See identical proteins and their annotated locations for NP_055500.1

Status: REVIEWED

Description

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

Source sequence(s)

AB034989, AC012181, AK223233, DA581153

Consensus CDS

CCDS10771.1

UniProtKB/Swiss-Prot

E9PGD1, O60644, Q15011, Q6IAN8, Q96D92

UniProtKB/TrEMBL

A0A2Z2EHH6, A8K6A0, A8K7S3, Q53FP9

Related

ENSP00000409555.2, ENST00000439977.7

Conserved Domains (1) summary

cd17118
Location:9 → 86

Ubl_HERP1; ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins

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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

56932142..56944864

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

62728473..62741195

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001010990.1: Suppressed sequence

Description

NM_001010990.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.