TENM3 teneurin transmembrane protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TENM3provided by HGNC
Official Full Name: teneurin transmembrane protein 3provided by HGNC
Primary source: HGNC:HGNC:29944
See related: Ensembl:ENSG00000218336 MIM:610083; AllianceGenome:HGNC:29944
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: ODZ3; TEN3; TNM3; ten-3; Ten-m3; MCOPCB9; MCOPS15
Summary: This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]
Annotation information: Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression: Broad expression in placenta (RPKM 7.1), brain (RPKM 4.3) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q34.3-q35.1

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (181447613..182803024)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (184789727..186144894)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (183065116..183724177)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Replicative verification of susceptibility genes previously identified from families with segregating developmental dysplasia of the hip.
Title: Replicative verification of susceptibility genes previously identified from families with segregating developmental dysplasia of the hip.
Ten-m/Odz3 regulates migration and differentiation of chondrogenic ATDC5 cells via RhoA-mediated actin reorganization.
Title: Ten-m/Odz3 regulates migration and differentiation of chondrogenic ATDC5 cells via RhoA-mediated actin reorganization.
Exome sequencing in patients with microphthalmia, anophthalmia, and coloboma (MAC) from a consanguineous population.
Title: Exome sequencing in patients with microphthalmia, anophthalmia, and coloboma (MAC) from a consanguineous population.
novel A to C transversion at position 183721398 on chromosome four found to co-segregate with the affected phenotype of developmental dysplasia of the hip
Title: Novel mutation in Teneurin 3 found to co-segregate in all affecteds in a multi-generation family with developmental dysplasia of the hip.
TENM3 missense mutation was identified in a patient with eye abnormalities and intellectual disability.
Title: Sequence variations in TENM3 gene causing eye anomalies with intellectual disability: Expanding the phenotypic spectrum.
This report supports the association of TENM3 mutations with colobomatous microphthalmia and expands the phenotypic spectrum associated with mutations in this gene
Title: Confirmation of TENM3 involvement in autosomal recessive colobomatous microphthalmia.
Null mutation in ODZ3 causes autosomal recessive microphthalmia in humans.
Title: Homozygous null mutation in ODZ3 causes microphthalmia in humans.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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
Microphthalmia, isolated, with coloboma 9 MedGen: C3554592 OMIM: 615145 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of preschool internalizing problems. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of multiplex schizophrenia pedigrees. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of smoking behaviours among Bangladeshi adults. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis of systolic blood pressure in children with sickle cell disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed
No evidence of gene-calcium interactions from genome-wide analysis of colorectal cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

D4S2560E (e-PCR)
- UniSTS:54795

RH66442 (e-PCR)
- UniSTS:30489

D4S600 (e-PCR)
- UniSTS:53786

D4S1109 (e-PCR)
- UniSTS:44070

D4S920 (e-PCR)
- UniSTS:26939

SHGC-59689 (e-PCR)
- UniSTS:68706

SHGC-83594 (e-PCR)
- UniSTS:95892

SHGC-33237 (e-PCR)
- UniSTS:15774

RH121048 (e-PCR)
- UniSTS:132269

D4S2592E (e-PCR)
- UniSTS:150987

RH120096 (e-PCR)
- UniSTS:132301

D4S3015 (e-PCR), detects polymorphism
- UniSTS:44797

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cell adhesion molecule binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein heterodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein homodimerization activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in camera-type eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of homophilic cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in axon	IEA Inferred from Electronic Annotation more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: teneurin-3

Names: ODZ3-like protein; odz, odd Oz/ten-m homolog 3; protein Odd Oz/ten-m homolog 3; tenascin-M3; testicular tissue protein Li 195

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_042859.1 RefSeqGene

Range

4972..564594

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001080477.4 → NP_001073946.1 teneurin-3 isoform 1

See identical proteins and their annotated locations for NP_001073946.1

Status: REVIEWED

Source sequence(s)

AB040888, AC079226, AC131943, AF195420, AK001336

Consensus CDS

CCDS47165.1

UniProtKB/Swiss-Prot

Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273

UniProtKB/TrEMBL

A0A140VJW8

Related

ENSP00000424226.1, ENST00000511685.6

Conserved Domains (11) summary

COG3209
Location:1613 → 2414

RhsA; Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only]

cd00054
Location:744 → 773

EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...

cd05819
Location:1175 → 1210

NHL; NHL repeat [structural motif]

TIGR01643
Location:1823 → 1863

YD_repeat_2x; YD repeat (two copies)

TIGR03696
Location:2318 → 2392

Rhs_assc_core; RHS repeat-associated core domain

pfam01500
Location:579 → 731

Keratin_B2; Keratin, high sulfur B2 protein

pfam06484
Location:11 → 308

Ten_N; Teneurin Intracellular Region

pfam07974
Location:522 → 544

EGF_2; EGF-like domain

pfam15636
Location:2617 → 2692

Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin

cl18310
Location:1146 → 1498

NHL; NHL repeat unit of beta-propeller proteins

cl19567
Location:697 → 738

DSL; Delta serrate ligand
NM_001415960.1 → NP_001402889.1 teneurin-3 isoform 2

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC109353, KF457841
NM_001415961.1 → NP_001402890.1 teneurin-3 isoform 3

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC109353, KF457841
NM_001415962.1 → NP_001402891.1 teneurin-3 isoform 4

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC109353, KF457841
NM_001415963.1 → NP_001402892.1 teneurin-3 isoform 5

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC109353, KF457841
NM_001415964.1 → NP_001402893.1 teneurin-3 isoform 6

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC109353, KF457841
NM_001415966.1 → NP_001402895.1 teneurin-3 isoform 7

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC108142, AC131943, KF457841
NM_001415967.1 → NP_001402896.1 teneurin-3 isoform 8

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC108142, AC131943, KF457841
NM_001415968.1 → NP_001402897.1 teneurin-3 isoform 9

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
NM_001415969.1 → NP_001402898.1 teneurin-3 isoform 10

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
NM_001415970.1 → NP_001402899.1 teneurin-3 isoform 10

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
NM_001415971.1 → NP_001402900.1 teneurin-3 isoform 1

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841

UniProtKB/Swiss-Prot

Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273

UniProtKB/TrEMBL

A0A140VJW8
NM_001415973.1 → NP_001402902.1 teneurin-3 isoform 1

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841

UniProtKB/Swiss-Prot

Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273

UniProtKB/TrEMBL

A0A140VJW8
NM_001415974.1 → NP_001402903.1 teneurin-3 isoform 11

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
NM_001415975.1 → NP_001402904.1 teneurin-3 isoform 11

Status: REVIEWED

Source sequence(s)

AC079226, AC093601, AC105288, AC108142, AC131943, KF457841
NM_001415976.1 → NP_001402905.1 teneurin-3 isoform 12

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC108142, AC131943, KF457841
NM_001415977.1 → NP_001402906.1 teneurin-3 isoform 12

Status: REVIEWED

Source sequence(s)

AC079226, AC105288, AC108142, AC131943, KF457841

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

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

181447613..182803024

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017008385.2 → XP_016863874.1 teneurin-3 isoform X1

Conserved Domains (8) summary

COG3209
Location:1783 → 2338

RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]

cd05819
Location:1184 → 1223

NHL; NHL repeat [structural motif]

TIGR03696
Location:2334 → 2408

Rhs_assc_core; RHS repeat-associated core domain

cl18310
Location:1155 → 1514

NHL; NHL repeat unit of beta-propeller proteins

pfam05593
Location:1631 → 1662

RHS_repeat; RHS Repeat

pfam06484
Location:11 → 308

Ten_N; Teneurin Intracellular Region

pfam15636
Location:2631 → 2708

Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin

NF033759
Location:466 → 801

exchanger_TraA; outer membrane exchange protein TraA
XM_017008389.2 → XP_016863878.1 teneurin-3 isoform X2
XM_017008390.2 → XP_016863879.1 teneurin-3 isoform X3
XM_017008391.2 → XP_016863880.1 teneurin-3 isoform X4
XM_017008394.2 → XP_016863883.1 teneurin-3 isoform X7
XM_047415944.1 → XP_047271900.1 teneurin-3 isoform X8
XM_047415933.1 → XP_047271889.1 teneurin-3 isoform X1
XM_017008386.2 → XP_016863875.1 teneurin-3 isoform X1

Conserved Domains (8) summary

COG3209
Location:1783 → 2338

RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]

cd05819
Location:1184 → 1223

NHL; NHL repeat [structural motif]

TIGR03696
Location:2334 → 2408

Rhs_assc_core; RHS repeat-associated core domain

cl18310
Location:1155 → 1514

NHL; NHL repeat unit of beta-propeller proteins

pfam05593
Location:1631 → 1662

RHS_repeat; RHS Repeat

pfam06484
Location:11 → 308

Ten_N; Teneurin Intracellular Region

pfam15636
Location:2631 → 2708

Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin

NF033759
Location:466 → 801

exchanger_TraA; outer membrane exchange protein TraA
XM_047415937.1 → XP_047271893.1 teneurin-3 isoform X5
XM_017008387.3 → XP_016863876.1 teneurin-3 isoform X1

Conserved Domains (8) summary

COG3209
Location:1783 → 2338

RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]

cd05819
Location:1184 → 1223

NHL; NHL repeat [structural motif]

TIGR03696
Location:2334 → 2408

Rhs_assc_core; RHS repeat-associated core domain

cl18310
Location:1155 → 1514

NHL; NHL repeat unit of beta-propeller proteins

pfam05593
Location:1631 → 1662

RHS_repeat; RHS Repeat

pfam06484
Location:11 → 308

Ten_N; Teneurin Intracellular Region

pfam15636
Location:2631 → 2708

Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin

NF033759
Location:466 → 801

exchanger_TraA; outer membrane exchange protein TraA
XM_017008388.2 → XP_016863877.1 teneurin-3 isoform X1

Conserved Domains (8) summary

COG3209
Location:1783 → 2338

RhsA; Uncharacterized conserved protein RhsA, contains 28 RHS repeats [General function prediction only]

cd05819
Location:1184 → 1223

NHL; NHL repeat [structural motif]

TIGR03696
Location:2334 → 2408

Rhs_assc_core; RHS repeat-associated core domain

cl18310
Location:1155 → 1514

NHL; NHL repeat unit of beta-propeller proteins

pfam05593
Location:1631 → 1662

RHS_repeat; RHS Repeat

pfam06484
Location:11 → 308

Ten_N; Teneurin Intracellular Region

pfam15636
Location:2631 → 2708

Tox-GHH; GHH signature containing HNH/Endo VII superfamily nuclease toxin

NF033759
Location:466 → 801

exchanger_TraA; outer membrane exchange protein TraA
XM_047415940.1 → XP_047271896.1 teneurin-3 isoform X6

UniProtKB/Swiss-Prot

Q5XUL9, Q96SY2, Q9NV77, Q9NVW1, Q9NZJ2, Q9P273

UniProtKB/TrEMBL

A0A140VJW8
XM_047415948.1 → XP_047271904.1 teneurin-3 isoform X10
XM_017008395.2 → XP_016863884.1 teneurin-3 isoform X9