SCAMP5 secretory carrier membrane protein 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCAMP5provided by HGNC
Official Full Name: secretory carrier membrane protein 5provided by HGNC
Primary source: HGNC:HGNC:30386
See related: Ensembl:ENSG00000198794 MIM:613766; AllianceGenome:HGNC:30386
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
Summary: Involved in positive regulation of cytokine production; regulation of vesicle-mediated transport; and response to endoplasmic reticulum stress. Located in Golgi apparatus; plasma membrane; and recycling endosome membrane. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in brain (RPKM 81.6), duodenum (RPKM 16.5) and 6 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q24.2

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (74995563..75021495)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (72865550..72891483)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (75287904..75313836)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Activation-induced colocalisation of SCAMP5 with IFNalpha in human plasmacytoid dendritic cells.
Title: Activation-induced colocalisation of SCAMP5 with IFNα in human plasmacytoid dendritic cells.
Investigations into SCAMP5, a candidate lupus risk gene expressed in plasmacytoid dendritic cells.
Title: Investigations into SCAMP5, a candidate lupus risk gene expressed in plasmacytoid dendritic cells.
SCAMP2/5 as diagnostic and prognostic markers for acute myeloid leukemia.
Title: SCAMP2/5 as diagnostic and prognostic markers for acute myeloid leukemia.
SCAMP5 plays a critical role in axonal trafficking and synaptic localization of NHE6 to adjust quantal size at glutamatergic synapses.
Title: SCAMP5 plays a critical role in axonal trafficking and synaptic localization of NHE6 to adjust quantal size at glutamatergic synapses.
work shows that dysfunction of SCAMP5 shifted the excitation/inhibition balance of the neuronal network in the brain, and the deficiency of SCAMP5 leads to pediatric epilepsy.
Title: Deficiency of SCAMP5 leads to pediatric epilepsy and dysregulation of neurotransmitter release in the brain.
scanp5 is predicted to play a role in neuronal vesicle trafficking and be involed in autism
Title: SCAMP5, NBEA and AMISYN: three candidate genes for autism involved in secretion of large dense-core vesicles.
exposure to ER stress increases SCAMP5 in the striatum, which positively regulates mtHTT aggregation via the endocytosis pathway
Title: SCAMP5 links endoplasmic reticulum stress to the accumulation of expanded polyglutamine protein aggregates via endocytosis inhibition.
SCAMP5 is involved in calcium-regulated exocytosis of signal peptide-containing cytokines, in cooperation with the SNARE machinery of secretory vesicles.
Title: Human SCAMP5, a novel secretory carrier membrane protein, facilitates calcium-triggered cytokine secretion by interaction with SNARE machinery.

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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 identifies loci affecting blood copper, selenium and zinc. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. 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

A001Y23 (e-PCR)
- UniSTS:36699

RH192 (e-PCR)
- UniSTS:8611

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in exocytosis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of calcium ion-dependent exocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cytokine production	IDA Inferred from Direct Assay more info	PubMed
involved_in protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to endoplasmic reticulum stress	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in recycling endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in recycling endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in synaptic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in trans-Golgi network membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: secretory carrier-associated membrane protein 5

Names: hSCAMP5

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_001178111.2 → NP_001171582.1 secretory carrier-associated membrane protein 5

See identical proteins and their annotated locations for NP_001171582.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1-3 encode the same protein.

Source sequence(s)

AK127480, BC024700, DA810757

Consensus CDS

CCDS45306.1

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5

Related

ENSP00000355387.6, ENST00000361900.10

Conserved Domains (1) summary

pfam04144
Location:6 → 179

SCAMP; SCAMP family
NM_001178112.2 → NP_001171583.1 secretory carrier-associated membrane protein 5

See identical proteins and their annotated locations for NP_001171583.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has an alternate exon in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.

Source sequence(s)

AK056438, BC024700

Consensus CDS

CCDS45306.1

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5

Conserved Domains (1) summary

pfam04144
Location:6 → 179

SCAMP; SCAMP family
NM_138967.4 → NP_620417.1 secretory carrier-associated membrane protein 5

See identical proteins and their annotated locations for NP_620417.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 5' UTR, compared to variant 1. Variants 1-3 encode the same protein.

Source sequence(s)

BC024700, DA810757

Consensus CDS

CCDS45306.1

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5

Related

ENSP00000406547.3, ENST00000425597.8

Conserved Domains (1) summary

pfam04144
Location:6 → 179

SCAMP; SCAMP family

RNA

NR_033660.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks multiple exons in the 5' UTR and coding region, compared to variant 1, which results in a frameshift and early stop codon. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated and the transcript is a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK301505, BC024700, DA810757

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_000015.10 Reference GRCh38.p14 Primary Assembly

Range

74995563..75021495

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047432218.1 → XP_047288174.1 secretory carrier-associated membrane protein 5 isoform X1
XM_006720421.2 → XP_006720484.1 secretory carrier-associated membrane protein 5 isoform X3

See identical proteins and their annotated locations for XP_006720484.1

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5

Conserved Domains (1) summary

pfam04144
Location:6 → 179

SCAMP; SCAMP family
XM_006720420.2 → XP_006720483.1 secretory carrier-associated membrane protein 5 isoform X2

Conserved Domains (1) summary

pfam04144
Location:24 → 197

SCAMP; SCAMP family
XM_047432219.1 → XP_047288175.1 secretory carrier-associated membrane protein 5 isoform X3

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

72865550..72891483

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054377438.1 → XP_054233413.1 secretory carrier-associated membrane protein 5 isoform X1
XM_054377440.1 → XP_054233415.1 secretory carrier-associated membrane protein 5 isoform X3

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5
XM_054377439.1 → XP_054233414.1 secretory carrier-associated membrane protein 5 isoform X2
XM_054377441.1 → XP_054233416.1 secretory carrier-associated membrane protein 5 isoform X3

UniProtKB/Swiss-Prot

B3KPJ7, B7Z762, D3DW71, Q8N3M4, Q8TAC9

UniProtKB/TrEMBL

A0A0A8K8F5