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TMEM260 transmembrane protein 260 [ Homo sapiens (human) ]

Gene ID: 54916, updated on 2-Nov-2024

Summary

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Official Symbol
TMEM260provided by HGNC
Official Full Name
transmembrane protein 260provided by HGNC
Primary source
HGNC:HGNC:20185
See related
Ensembl:ENSG00000070269 MIM:617449; AllianceGenome:HGNC:20185
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
SHDRA; C14orf101
Summary
Enables dolichyl-phosphate-mannose-protein mannosyltransferase activity. Involved in protein maturation. Is active in endoplasmic reticulum membrane. Implicated in T-cell non-Hodgkin lymphoma; non-Hodgkin lymphoma; and stomach cancer. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 3.9), ovary (RPKM 3.6) and 25 other tissues See more
Orthologs
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Genomic context

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See TMEM260 in Genome Data Viewer
Location:
14q22.3
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (56579525..56663165)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (50785268..50870723)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (57046516..57116233)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2284 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:56880383-56881582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56913685-56914290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56914291-56914896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:56919397-56919898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:56919899-56920398 Neighboring gene uncharacterized LOC101927690 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34259 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34268 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34274 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:56991474-56992081 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34296 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34318 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:57028256-57028447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5790 Neighboring gene NANOG hESC enhancer GRCh37_chr14:57115102-57115779 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:57132632-57133831 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34331 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:57154864-57155025 Neighboring gene uncharacterized LOC124903433 Neighboring gene ribosomal protein L36a pseudogene 1

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 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. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease. Inoue T, et al. J Hum Genet, 2024 May. PMID 38409496, Free PMC Article
  2. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population. Yaoita H, et al. J Hum Genet, 2024 May. PMID 38351237, Free PMC Article
  3. Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects. Pagnamenta AT, et al. Clin Genet, 2022 Jan. PMID 34612517
  4. Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome. Ta-Shma A, et al. Am J Hum Genet, 2017 Apr 6. PMID 28318500, Free PMC Article
  5. A polymorphism at the microRNA binding site in the 3' untranslated region of C14orf101 is associated with non-Hodgkin lymphoma overall survival. Yang B, et al. Cancer Genet, 2014 Apr. PMID 24831772

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease.
    Title: The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease.
  2. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population.
    Title: Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population.
  3. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase.
    Title: The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase.
  4. Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects.
    Title: Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects.
  5. Study showed that truncating mutations in TMEM260 cause a syndrome characterized by central nervous sustem, cardiac, renal, and axial skeletal defects. Notably, the homozygous truncating mutations found in the two families affected specifically one of the two splice isoforms generated by this locus, arguing specificity in the phenotypic driver.
    Title: Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome.
  6. Data indicate that rs4901706, located in the 3' UTR of C14orf101, was shown to be independently related to overall survival in non-Hodgkin lymphoma (NHL).
    Title: A polymorphism at the microRNA binding site in the 3' untranslated region of C14orf101 is associated with non-Hodgkin lymphoma overall survival.
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
Structural heart defects and renal anomalies syndrome
MedGen: C4479549 OMIM: 617478 GeneReviews: Not available
not available

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20392

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein O-linked mannosylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein maturation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
protein O-mannosyl-transferase TMEM260
Names
UPF0679 protein C14orf101
NP_060269.3
XP_011535153.1
XP_011535154.1
XP_047287449.1
XP_047287450.1
XP_047287451.1
XP_047287452.1
XP_047287453.1
XP_047287454.1
XP_054232221.1
XP_054232222.1
XP_054232223.1
XP_054232224.1
XP_054232225.1
XP_054232226.1
XP_054232227.1
XP_054232228.1

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)

  1. NM_017799.4 → NP_060269.3  protein O-mannosyl-transferase TMEM260 precursor

    See identical proteins and their annotated locations for NP_060269.3

    Status: VALIDATED

    Source sequence(s)
    AK023885, AK056291, AL161757, BX647387
    Consensus CDS
    CCDS9727.2
    UniProtKB/Swiss-Prot
    A8KAN4, B3KPF5, Q0VAA1, Q86XE1, Q9NX78
    UniProtKB/TrEMBL
    Q0IJ48
    Related
    ENSP00000261556.6, ENST00000261556.11
    Conserved Domains (1) summary
    pfam11028
    Location:52 → 206
    DUF2723; Protein of unknown function (DUF2723)

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

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    56579525..56663165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431494.1 → XP_047287450.1  protein O-mannosyl-transferase TMEM260 isoform X3

  2. XM_011536851.3 → XP_011535153.1  protein O-mannosyl-transferase TMEM260 isoform X1

    UniProtKB/TrEMBL
    Q0IJ48
    Conserved Domains (1) summary
    pfam11028
    Location:52 → 206
    DUF2723; Protein of unknown function (DUF2723)

  3. XM_047431497.1 → XP_047287453.1  protein O-mannosyl-transferase TMEM260 isoform X6

    Related
    ENSP00000441934.1, ENST00000538838.5

  4. XM_047431495.1 → XP_047287451.1  protein O-mannosyl-transferase TMEM260 isoform X4

  5. XM_047431496.1 → XP_047287452.1  protein O-mannosyl-transferase TMEM260 isoform X5

  6. XM_047431493.1 → XP_047287449.1  protein O-mannosyl-transferase TMEM260 isoform X3

  7. XM_011536852.2 → XP_011535154.1  protein O-mannosyl-transferase TMEM260 isoform X2

  8. XM_047431498.1 → XP_047287454.1  protein O-mannosyl-transferase TMEM260 isoform X7

RNA

  1. XR_007064017.1 RNA Sequence

  2. XR_007064018.1 RNA Sequence

  3. XR_007064019.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    50785268..50870723
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054376249.1 → XP_054232224.1  protein O-mannosyl-transferase TMEM260 isoform X3

  2. XM_054376246.1 → XP_054232221.1  protein O-mannosyl-transferase TMEM260 isoform X1

  3. XM_054376252.1 → XP_054232227.1  protein O-mannosyl-transferase TMEM260 isoform X6

  4. XM_054376250.1 → XP_054232225.1  protein O-mannosyl-transferase TMEM260 isoform X4

  5. XM_054376251.1 → XP_054232226.1  protein O-mannosyl-transferase TMEM260 isoform X5

  6. XM_054376248.1 → XP_054232223.1  protein O-mannosyl-transferase TMEM260 isoform X3

  7. XM_054376247.1 → XP_054232222.1  protein O-mannosyl-transferase TMEM260 isoform X2

  8. XM_054376253.1 → XP_054232228.1  protein O-mannosyl-transferase TMEM260 isoform X7

RNA

  1. XR_008488876.1 RNA Sequence

  2. XR_008488877.1 RNA Sequence

  3. XR_008488878.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NX78.3 GenPept UniProtKB/Swiss-Prot:Q9NX78

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