CCDC47 coiled-coil domain containing 47 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCDC47provided by HGNC
Official Full Name: coiled-coil domain containing 47provided by HGNC
Primary source: HGNC:HGNC:24856
See related: Ensembl:ENSG00000108588 MIM:618260; AllianceGenome:HGNC:24856
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: THNS; GK001; MSTP041
Summary: Enables protein folding chaperone and ribosome binding activity. Involved in ERAD pathway; endoplasmic reticulum calcium ion homeostasis; and protein insertion into ER membrane. Located in endoplasmic reticulum. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in colon (RPKM 44.7), duodenum (RPKM 34.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q23.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (63745255..63773597, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (64616174..64644500, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (61822615..61850957, complement)

Chromosome 17 - NC_000017.11 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?

these findings suggested that calumin serves to maintain the yolk sac integrity through participation in the ERAD activity, contributing to embryonic development.
Title: Contribution of calumin to embryogenesis through participation in the endoplasmic reticulum-associated degradation activity.

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

Associated conditions

Description	Tests
Trichohepatoneurodevelopmental syndrome MedGen: C4748898 OMIM: 618268 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr is identified to have a physical interaction with coiled-coil domain containing 47 (CCDC47) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D17S1628 (e-PCR)
- UniSTS:153642

RH47195 (e-PCR)
- UniSTS:2865

RH103266 (e-PCR)
- UniSTS:97598

RH80257 (e-PCR)
- UniSTS:84352

RH45286 (e-PCR)
- UniSTS:61328

SHGC-11242 (e-PCR)
- UniSTS:71867

D17S1437E (e-PCR)
- UniSTS:150475

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein folding chaperone	IDA Inferred from Direct Assay more info	PubMed
enables ribosome binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in ER overload response	IEA Inferred from Electronic Annotation more info
involved_in ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multi-pass transmembrane protein insertion into ER membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in osteoblast differentiation	HDA more info	PubMed
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in protein folding	IEA Inferred from Electronic Annotation more info
involved_in protein insertion into ER membrane	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
part_of multi-pass translocon complex	IDA Inferred from Direct Assay more info	PubMed
part_of multi-pass translocon complex	IPI Inferred from Physical Interaction more info	PubMed
part_of protein folding chaperone complex	IPI Inferred from Physical Interaction more info	PubMed
located_in rough endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PAT complex subunit CCDC47

Names: Calumin; coiled-coil domain-containing protein 47

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_020198.3 → NP_064583.2 PAT complex subunit CCDC47 precursor

See identical proteins and their annotated locations for NP_064583.2

Status: VALIDATED

Source sequence(s)

AF226054, AK027844, BC001300, DB222124

Consensus CDS

CCDS11643.1

UniProtKB/Swiss-Prot

B2RAS8, D3DU20, Q96A33, Q96D00, Q96JZ7, Q9H3E4, Q9NRG3

Related

ENSP00000225726.5, ENST00000225726.10

Conserved Domains (2) summary

PRK05901
Location:18 → 115

PRK05901; RNA polymerase sigma factor; Provisional

pfam07946
Location:135 → 467

DUF1682; Protein of unknown function (DUF1682)

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_000017.11 Reference GRCh38.p14 Primary Assembly

Range

63745255..63773597 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005257527.3 → XP_005257584.1 PAT complex subunit CCDC47 isoform X1

See identical proteins and their annotated locations for XP_005257584.1

UniProtKB/Swiss-Prot

B2RAS8, D3DU20, Q96A33, Q96D00, Q96JZ7, Q9H3E4, Q9NRG3

Conserved Domains (2) summary

PRK05901
Location:18 → 115

PRK05901; RNA polymerase sigma factor; Provisional

pfam07946
Location:135 → 467

DUF1682; Protein of unknown function (DUF1682)