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Intellectual disability

Gene: TENM3

Amber List (moderate evidence)

TENM3 (teneurin transmembrane protein 3)
EnsemblGeneIds (GRCh38): ENSG00000218336
EnsemblGeneIds (GRCh37): ENSG00000218336
OMIM: 610083, Gene2Phenotype
TENM3 is in 5 panels

2 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review - sufficient unrelated cases with an ID phenotype.
Created: 24 Aug 2020, 10:50 a.m. | Last Modified: 24 Aug 2020, 10:50 a.m.
Panel Version: 3.263
Associated with phenotype in OMIM, and a probable gene for Colobomatous microphthalmia in G2P.

PMID: 22766609 (2012) - Two affected sibs from a consanguineous Saudi family, with nonsyndromic bilateral microphthalmia, iris and retinal coloboma, and microcornea. Normal cognitive development was noted in both sibs. A homozygous 1 bp insertion (c.2083dup, p.T695Nfs*5) in the TENM3 gene, causing a frameshift predicted to result in premature truncation of the resulting protein, segregated with the phenotype. No other pathogenic variant were identified in any of the known microphthalmia genes.

PMID: 27103084 (2016) - In a patient with bilateral colobomatous microphthalmia authors identified a segregating homozygous splice site variant (c.2968‐2A>T, p.Val990Cysfs*13) in the TENM3 gene. His development was delayed, and he entered a specialised institution at the age of eight because of his apparent ID.

PMID: 30513139 (2018) - In two sisters with ocular coloboma and microcornea, but without microphthalmia, WES revealed a homozygous TENM3 variant (c.1857T>A, p. Cys619*). Sanger sequencing confirmed the parents were heterozygous carriers. Patient cells were not available for functional study of the variant. The older child (5.5 years old) was said to have global developmental delay; while the younger child (4 years 3 months old) had mild motor delay and spoke only few words, but cognition was reported normal.

PMID: 29753094 (2019) - 9-year-old boy with right eye microphthalmia, sclerocornea of both eyes, anterior segment dysgenesis, and severe global developmental delay, associated with compound heterozygous variants ([c.4046C>G, p.Ala1349Gly] ; [c.7687C>T, p.Arg2563Trp]) in the TENM3 gene. The p.Ala1349Gly variant was found in a heterozygous state in the proband's unaffected father and brother; however, the p.Arg2563Trp variant was not present in either parent, suggesting mosaicism in the mother or a de novo occurrence in the proband.
Created: 24 Aug 2020, 10:33 a.m. | Last Modified: 24 Aug 2020, 10:33 a.m.
Panel Version: 3.262

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Microphthalmia, syndromic 15, 615145; ?Microphthalmia, isolated, with coloboma 9, 615145


Zornitza Stark (Australian Genomics)

Green List (high evidence)

At least four unrelated families described with syndromic microphthalmia and bi-allelic variants in this gene, ID is part of the phenotype.
Sources: Expert list
Created: 1 Mar 2020, 12:38 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Microphthalmia, syndromic 15, MIM#615145; coloboma


Variants in this GENE are reported as part of current diagnostic practice


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Amber
  • Microphthalmia, syndromic 15, MIM#615145
  • coloboma
Clinvar variants
Variants in TENM3
Panels with this gene

History Filter Activity

24 Aug 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: tenm3 has been classified as Amber List (Moderate Evidence).

24 Aug 2020, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review tag was added to gene: TENM3.

1 Mar 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Australian Genomics)

gene: TENM3 was added gene: TENM3 was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: TENM3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TENM3 were set to 30513139; 22766609; 27103084; 29753094 Phenotypes for gene: TENM3 were set to Microphthalmia, syndromic 15, MIM#615145; coloboma Review for gene: TENM3 was set to GREEN gene: TENM3 was marked as current diagnostic