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TTC39C tetratricopeptide repeat domain 39C [ Homo sapiens (human) ]

Gene ID: 125488, updated on 5-Mar-2024

Summary

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Official Symbol
TTC39Cprovided by HGNC
Official Full Name
tetratricopeptide repeat domain 39Cprovided by HGNC
Primary source
HGNC:HGNC:26595
See related
Ensembl:ENSG00000168234 AllianceGenome:HGNC:26595
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
HsT2697; C18orf17
Summary
Predicted to be involved in cilium assembly and otolith morphogenesis. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in liver (RPKM 7.1), skin (RPKM 3.6) and 20 other tissues See more
Orthologs
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Genomic context

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See TTC39C in Genome Data Viewer
Location:
18q11.2
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (23992887..24135600)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (24187146..24329927)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (21572851..21715564)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21299932-21300432 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:21300433-21300933 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21305921-21306891 Neighboring gene ribosomal protein L23a pseudogene 77 Neighboring gene laminin subunit alpha 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21427116-21427961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13165 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:21452354-21453553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:21531393-21532253 Neighboring gene MPRA-validated peak3071 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13166 Neighboring gene long intergenic non-protein coding RNA 2958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9361 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9362 Neighboring gene TTC39C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13170 Neighboring gene Sharpr-MPRA regulatory region 15364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13171 Neighboring gene RNA, U5A small nuclear 6, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 452 Neighboring gene calcium binding tyrosine phosphorylation regulated Neighboring gene oxysterol binding protein like 1A

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. Ttc39c is a potential target for the treatment of lung cancer. Rong H, et al. BMC Pulm Med, 2022 Oct 27. PMID 36303158, Free PMC Article
  2. A genome-wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity. Meng W, et al. Ophthalmic Genet, 2019 Jun. PMID 31264924
  3. DNA sequence and analysis of human chromosome 18. Nusbaum C, et al. Nature, 2005 Sep 22. PMID 16177791
  4. The functional landscape of Hsp27 reveals new cellular processes such as DNA repair and alternative splicing and proposes novel anticancer targets. Katsogiannou M, et al. Mol Cell Proteomics, 2014 Dec. PMID 25277244, Free PMC Article
  5. Elucidation of the BMI1 interactome identifies novel regulatory roles in glioblastoma. Freire-Benéitez V, et al. NAR Cancer, 2021 Mar. PMID 34316702, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ttc39c is a potential target for the treatment of lung cancer.
    Title: Ttc39c is a potential target for the treatment of lung cancer.
  2. Single Nucleotide Polymorphism in the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity.
    Title: A genome-wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity.
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

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

  • FLJ33761, FLJ90394

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in otolith morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
tetratricopeptide repeat protein 39C
Names
TPR repeat protein 39C

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_001135993.2 → NP_001129465.1  tetratricopeptide repeat protein 39C isoform 1

    See identical proteins and their annotated locations for NP_001129465.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC010754, AC090772, KF456356
    Consensus CDS
    CCDS45839.1
    UniProtKB/Swiss-Prot
    B7WP63, J3QRR1, Q0VAJ2, Q8N284, Q8N584
    Related
    ENSP00000323645.3, ENST00000317571.8
    Conserved Domains (1) summary
    pfam10300
    Location:34 → 498
    DUF3808; Protein of unknown function (DUF3808)

  2. NM_001243425.2 → NP_001230354.1  tetratricopeptide repeat protein 39C isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 3' UTR and lacks a large portion of the 3' coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC016833
    Consensus CDS
    CCDS58616.1
    UniProtKB/Swiss-Prot
    Q8N584
    Related
    ENSP00000464344.1, ENST00000584250.1
    Conserved Domains (1) summary
    pfam10300
    Location:34 → 58
    DUF3808; Protein of unknown function (DUF3808)

  3. NM_001292030.2 → NP_001278959.1  tetratricopeptide repeat protein 39C isoform 4 precursor

    See identical proteins and their annotated locations for NP_001278959.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks part of the 5' coding region, contains an alternate 5'-terminal exon, and uses an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC090772, KF456356
    Consensus CDS
    CCDS77165.1
    UniProtKB/TrEMBL
    B7Z3X0, G3V1P2
    Related
    ENSP00000443016.1, ENST00000540918.2
    Conserved Domains (1) summary
    pfam10300
    Location:11 → 191
    DUF3808; Protein of unknown function (DUF3808)

  4. NM_153211.4 → NP_694943.2  tetratricopeptide repeat protein 39C isoform 2

    See identical proteins and their annotated locations for NP_694943.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains a distinct 5' UTR, lacks an in-frame portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC010754, AC090772, KF456356
    Consensus CDS
    CCDS32804.1
    UniProtKB/Swiss-Prot
    Q8N584
    Related
    ENSP00000306598.6, ENST00000304621.10
    Conserved Domains (1) summary
    pfam10300
    Location:1 → 437
    DUF3808; Protein of unknown function (DUF3808)

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    23992887..24135600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437297.1 → XP_047293253.1  tetratricopeptide repeat protein 39C isoform X3

  2. XM_047437298.1 → XP_047293254.1  tetratricopeptide repeat protein 39C isoform X3

  3. XM_047437296.1 → XP_047293252.1  tetratricopeptide repeat protein 39C isoform X1

  4. XM_011525814.4 → XP_011524116.1  tetratricopeptide repeat protein 39C isoform X2

    Conserved Domains (1) summary
    pfam10300
    Location:34 → 462
    DUF3808; Protein of unknown function (DUF3808)

  5. XM_006722392.4 → XP_006722455.1  tetratricopeptide repeat protein 39C isoform X4

    Conserved Domains (1) summary
    pfam10300
    Location:34 → 329
    DUF3808; Protein of unknown function (DUF3808)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    24187146..24329927
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318197.1 → XP_054174172.1  tetratricopeptide repeat protein 39C isoform X3

  2. XM_054318198.1 → XP_054174173.1  tetratricopeptide repeat protein 39C isoform X3

  3. XM_054318195.1 → XP_054174170.1  tetratricopeptide repeat protein 39C isoform X1

  4. XM_054318196.1 → XP_054174171.1  tetratricopeptide repeat protein 39C isoform X2

  5. XM_054318199.1 → XP_054174174.1  tetratricopeptide repeat protein 39C isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N584.2 GenPept UniProtKB/Swiss-Prot:Q8N584

Gene LinkOut

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