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C3orf52 chromosome 3 open reading frame 52 [ Homo sapiens (human) ]

Gene ID: 79669, updated on 7-Apr-2024

Summary

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Official Symbol
C3orf52provided by HGNC
Official Full Name
chromosome 3 open reading frame 52provided by HGNC
Primary source
HGNC:HGNC:26255
See related
Ensembl:ENSG00000114529 MIM:611956; AllianceGenome:HGNC:26255
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
TTMP; HYPT15
Summary
Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in skin (RPKM 9.2), thyroid (RPKM 5.4) and 15 other tissues See more
Orthologs
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Genomic context

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Location:
3q13.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (112086389..112136381)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (114807509..114857494)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (111805236..111837057)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene riboflavin kinase-like Neighboring gene transmembrane serine protease 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:111804898-111805414 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:111820488-111821687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20232 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20233 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20235 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111845355-111845988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20236 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20237 Neighboring gene microRNA 567 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111855415-111855934 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:111855935-111856453 Neighboring gene germinal center associated signaling and motility Neighboring gene TGF-beta induced lncRNA Neighboring gene solute carrier family 9 member C1 Neighboring gene uncharacterized LOC124909407 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:111904045-111904638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:111904639-111905231 Neighboring gene INAVA pseudogene 1 Neighboring gene ubiquitination factor E4A (UFD2 homolog, yeast) pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Update of recent findings in genetic hair disorders. Hayashi R, et al. J Dermatol, 2022 Jan. PMID 34676598
  2. A novel homozygous frameshift variant in the C3orf52 gene underlying isolated hair loss in a consanguineous family. Shah K, et al. Eur J Dermatol, 2021 Jun 1. PMID 34309526
  3. Identification and in silico characterization of a novel gene: TPA induced trans-membrane protein. Chan CY, et al. Biochem Biophys Res Commun, 2005 Apr 8. PMID 15737651
  4. Loss-of-function variants in C3ORF52 result in localized autosomal recessive hypotrichosis. Malki L, et al. Genet Med, 2020 Jul. PMID 32336749, Free PMC Article
  5. Systematic identification of pathological lamin A interactors. Dittmer TA, et al. Mol Biol Cell, 2014 May. PMID 24623722, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A novel homozygous frameshift variant in the C3orf52 gene underlying isolated hair loss in a consanguineous family.
    Title: A novel homozygous frameshift variant in the C3orf52 gene underlying isolated hair loss in a consanguineous family.
  2. Loss-of-function variants in C3ORF52 result in localized autosomal recessive hypotrichosis.
    Title: Loss-of-function variants in C3ORF52 result in localized autosomal recessive hypotrichosis.
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
Hypotrichosis 15
MedGen: C5774279 OMIM: 620177 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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23186

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
TPA-induced transmembrane protein
Names
TPA induced trans-membrane protein
novel endoplasmic reticulum transmembrane protein

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)

  1. NM_001171747.2 → NP_001165218.1  TPA-induced transmembrane protein isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) is the shorter transcript but encodes the longer isoform (1).
    Source sequence(s)
    AC128688, AK298076, AK303588
    Consensus CDS
    CCDS54620.1
    UniProtKB/TrEMBL
    H7C5J7
    Related
    ENSP00000399392.2, ENST00000431717.6

  2. NM_024616.3 → NP_078892.3  TPA-induced transmembrane protein isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has two additional coding exons in the 3' region, as compared to variant 1. The resulting isoform (2) is shorter and has a different C-terminus, as compared to isoform 1.
    Source sequence(s)
    AC024887, AC128688
    Consensus CDS
    CCDS46887.1
    UniProtKB/Swiss-Prot
    B4DNV2, B4E0Z2, Q5BVD1, Q96AJ4, Q9H5Q1
    Related
    ENSP00000264848.5, ENST00000264848.10

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

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    112086389..112136381
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_924171.4 RNA Sequence

  2. XR_007095726.1 RNA Sequence

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_019805492.1 Reference GRCh38.p14 PATCHES

    Range
    1..1500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    114807509..114857494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_008486793.1 RNA Sequence

  2. XR_008486794.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5BVD1.2 GenPept UniProtKB/Swiss-Prot:Q5BVD1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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