TMTC4 transmembrane O-mannosyltransferase targeting cadherins 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TMTC4provided by HGNC
Official Full Name: transmembrane O-mannosyltransferase targeting cadherins 4provided by HGNC
Primary source: HGNC:HGNC:25904
See related: Ensembl:ENSG00000125247 MIM:618203; AllianceGenome:HGNC:25904
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DFNB122
Summary: This gene encodes a transmembrane protein that belongs to family of proteins containing an N-terminal transmembrane domain and a C-terminal tetratricopeptide repeat (TPR) domain. TPR domains mediate protein-protein interactions in various cellular processes, such as synaptic vesicle fusion, protein folding, and protein translocation. A pseudogene of this gene has been defined on chromosome 5. [provided by RefSeq, Apr 2017]
Expression: Ubiquitous expression in brain (RPKM 8.0), testis (RPKM 5.8) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q32.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (100603625..100675075, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (99818881..99890298, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (101255879..101327049, complement)

Chromosome 13 - NC_000013.11 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?

TMTC4 is a hair cell-specific human deafness gene.
Title: TMTC4 is a hair cell-specific human deafness gene.
Transmembrane and Tetratricopeptide Repeat Containing 4 Is a Novel Diagnostic Marker for Prostate Cancer with High Specificity and Sensitivity.
Title: Transmembrane and Tetratricopeptide Repeat Containing 4 Is a Novel Diagnostic Marker for Prostate Cancer with High Specificity and Sensitivity.
Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.
Title: Conserved sequence motifs in human TMTC1, TMTC2, TMTC3, and TMTC4, new O-mannosyltransferases from the GT-C/PMT clan, are rationalized as ligand binding sites.

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
Deafness, autosomal recessive 122 MedGen: CN376840 OMIM: 620714 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH47425 (e-PCR)
- UniSTS:40

A007J11 (e-PCR)
- UniSTS:17002

NIB1408 (e-PCR)
- UniSTS:47818

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATPase binding	IPI Inferred from Physical Interaction more info	PubMed
enables dolichyl-phosphate-mannose-protein mannosyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables mannosyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum unfolded protein response	IBA Inferred from Biological aspect of Ancestor more info
involved_in outer hair cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endoplasmic reticulum calcium ion concentration	IEA Inferred from Electronic Annotation more info
involved_in protein O-linked mannosylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein O-linked mannosylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IEA Inferred from Electronic Annotation more info

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	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein O-mannosyl-transferase TMTC4

Names: transmembrane and TPR repeat-containing protein 4; transmembrane and tetratricopeptide repeat containing 4

NP_001073137.1

EC 2.4.1.109

NP_001273382.1

EC 2.4.1.109

NP_001337500.1

EC 2.4.1.109

NP_001337501.1

EC 2.4.1.109

NP_001337503.1

EC 2.4.1.109

NP_001337505.1

EC 2.4.1.109

NP_001337506.1

EC 2.4.1.109

NP_116202.2

EC 2.4.1.109

XP_011519424.1

EC 2.4.1.109

XP_047286661.1

EC 2.4.1.109

XP_047286662.1

EC 2.4.1.109

XP_054231045.1

EC 2.4.1.109

XP_054231046.1

EC 2.4.1.109

XP_054231047.1

EC 2.4.1.109

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.

Genomic

NG_053145.1 RefSeqGene

Range

5299..76469

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001079669.4 → NP_001073137.1 protein O-mannosyl-transferase TMTC4 isoform 2

See identical proteins and their annotated locations for NP_001073137.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (2) is shorter than isoform 4. Both variants 2 and 5 encode the same isoform (2).

Source sequence(s)

AL359085, AW513848, BX647956

Consensus CDS

CCDS41904.1

UniProtKB/Swiss-Prot

A6NLI7, B7Z666, Q5T4D3, Q5T4D4, Q5T4D5, Q5T4D6, Q8WV63, Q96SU8

UniProtKB/TrEMBL

A8K2T0

Related

ENSP00000365408.3, ENST00000376234.7

Conserved Domains (3) summary

COG0457
Location:481 → 717

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:482 → 510

TPR; TPR repeat [structural motif]

pfam08409
Location:294 → 366

DUF1736; Domain of unknown function (DUF1736)
NM_001286453.3 → NP_001273382.1 protein O-mannosyl-transferase TMTC4 isoform 3

See identical proteins and their annotated locations for NP_001273382.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, contains multiple differences in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AF339792, AK299859, AL359085, AW513848, DC377683

Consensus CDS

CCDS66575.1

UniProtKB/TrEMBL

A8K2T0

Related

ENSP00000365409.2, ENST00000328767.9

Conserved Domains (7) summary

smart00028
Location:473 → 506

TPR; Tetratricopeptide repeats

sd00006
Location:371 → 399

TPR; TPR repeat [structural motif]

pfam00515
Location:439 → 472

TPR_1; Tetratricopeptide repeat

pfam07719
Location:371 → 404

TPR_2; Tetratricopeptide repeat

pfam08409
Location:181 → 255

DUF1736; Domain of unknown function (DUF1736)

pfam13414
Location:370 → 436

TPR_11; TPR repeat

pfam13431
Location:393 → 426

TPR_17; Tetratricopeptide repeat
NM_001350571.2 → NP_001337500.1 protein O-mannosyl-transferase TMTC4 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) represents the longest transcript and encodes the longest isoform (4).

Source sequence(s)

AL359085

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:558 → 794

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:559 → 587

TPR; TPR repeat [structural motif]

pfam08409
Location:369 → 443

DUF1736; Domain of unknown function (DUF1736)
NM_001350572.2 → NP_001337501.1 protein O-mannosyl-transferase TMTC4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (2) is shorter than isoform 4. Both variants 2 and 5 encode the same isoform (2).

Source sequence(s)

AL359085

Consensus CDS

CCDS41904.1

UniProtKB/Swiss-Prot

A6NLI7, B7Z666, Q5T4D3, Q5T4D4, Q5T4D5, Q5T4D6, Q8WV63, Q96SU8

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:481 → 717

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:482 → 510

TPR; TPR repeat [structural motif]

pfam08409
Location:294 → 366

DUF1736; Domain of unknown function (DUF1736)
NM_001350574.2 → NP_001337503.1 protein O-mannosyl-transferase TMTC4 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (5) is has a shorter and distinct N-terminus compared to isoform 4.

Source sequence(s)

AL359085

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:539 → 775

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:540 → 568

TPR; TPR repeat [structural motif]

pfam08409
Location:350 → 424

DUF1736; Domain of unknown function (DUF1736)
NM_001350576.2 → NP_001337505.1 protein O-mannosyl-transferase TMTC4 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an alternate in-frame exon in the 5' coding region, compared to variant 4. The encoded isoform (6) is shorter than isoform 4.

Source sequence(s)

AL359085

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:498 → 734

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:499 → 527

TPR; TPR repeat [structural motif]

pfam08409
Location:313 → 383

DUF1736; Domain of unknown function (DUF1736)
NM_001350577.2 → NP_001337506.1 protein O-mannosyl-transferase TMTC4 isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (8) differs in the 5' UTR, has multiple coding region differences, and initiates translation at a downstream start codon, compared to variant 4. The encoded isoform (7) is shorter than isoform 4.

Source sequence(s)

AL359085

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:479 → 715

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:480 → 508

TPR; TPR repeat [structural motif]

pfam08409
Location:294 → 364

DUF1736; Domain of unknown function (DUF1736)
NM_032813.5 → NP_116202.2 protein O-mannosyl-transferase TMTC4 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks an alternate in-frame exon in the 5' coding region, compared to variant 4. The encoded isoform (1) is shorter than isoform 4.

Source sequence(s)

AK056409, AL359085, AW513848, BG830268, CV029196, DA368450

Consensus CDS

CCDS9497.2

UniProtKB/TrEMBL

A8K2T0

Related

ENSP00000343871.5, ENST00000342624.10

Conserved Domains (7) summary

smart00028
Location:603 → 636

TPR; Tetratricopeptide repeats

sd00006
Location:501 → 529

TPR; TPR repeat [structural motif]

pfam00515
Location:569 → 602

TPR_1; Tetratricopeptide repeat

pfam07719
Location:501 → 534

TPR_2; Tetratricopeptide repeat

pfam08409
Location:311 → 385

DUF1736; Domain of unknown function (DUF1736)

pfam13414
Location:500 → 566

TPR_11; TPR repeat

pfam13431
Location:523 → 556

TPR_17; Tetratricopeptide repeat

RNA

NR_146794.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (9) lacks two alternate exons in the 5' region and contains an alternate exon in the 3' region, compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL359085

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_000013.11 Reference GRCh38.p14 Primary Assembly

Range

100603625..100675075 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047430706.1 → XP_047286662.1 protein O-mannosyl-transferase TMTC4 isoform X3
XM_011521122.4 → XP_011519424.1 protein O-mannosyl-transferase TMTC4 isoform X1

See identical proteins and their annotated locations for XP_011519424.1

UniProtKB/TrEMBL

A8K2T0

Conserved Domains (3) summary

COG0457
Location:558 → 794

TPR; Tetratricopeptide (TPR) repeat [General function prediction only]

sd00006
Location:559 → 587

TPR; TPR repeat [structural motif]

pfam08409
Location:369 → 443

DUF1736; Domain of unknown function (DUF1736)
XM_047430705.1 → XP_047286661.1 protein O-mannosyl-transferase TMTC4 isoform X2