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Intellectual disability

Gene: TM2D3

Amber List (moderate evidence)
TM2D3 (TM2 domain containing 3)
EnsemblGeneIds (GRCh38): ENSG00000184277
EnsemblGeneIds (GRCh37): ENSG00000184277
OMIM: 610014, Gene2Phenotype
TM2D3 is in 3 panels

1 review

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are four unrelated patients reported with severe global developmental delay. Hence, this gene can be promoted to green rating in the next GMS update.
Created: 2 Jan 2026, 9:38 p.m. | Last Modified: 2 Jan 2026, 9:38 p.m.
Panel Version: 9.213
PMID:40449487 (2025) reported four unrelated individuals with overlapping clinical presentations, including microcephaly, severe global developmental delay with absent speech, autistic features, heart malformation, and dysmorphic facial features. Severe GDD was reported in all four patients. They were all identified with homozygous or compound heterozygous variants in TM2D3 gene via exome sequencing.

There is also functional evidence available from SNB75 TM2D3-knockout cells as well as skin fibroblasts from affected individuals harbouring the recurrent c.503G>A (p.Gly168Asp) allele.

This gene has been associated with relevant phenotype in OMIM (MIM #621379, last accessed 02 January 2026) and Gene2Phenotype (with 'moderate' rating on DD panel), but not yet in ClinGen.
Sources: Literature
Created: 2 Jan 2026, 9:35 p.m. | Last Modified: 2 Jan 2026, 9:36 p.m.
Panel Version: 9.212

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurocardiorenal malformation syndrome, OMIM:621379

Publications

Created: 2 Jan 2026, 9:35 p.m.
Last Modified: 2 Jan 2026, 9:36 p.m.
Panel version: 9.212

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Neurocardiorenal malformation syndrome, OMIM:621379
Tags
Q1_26_promote_green
OMIM
610014
Clinvar variants
Variants in TM2D3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

2 Jan 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: tm2d3 has been classified as Amber List (Moderate Evidence).

2 Jan 2026, Gel status: 1

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_26_promote_green tag was added to gene: TM2D3.

2 Jan 2026, Gel status: 1

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

Achchuthan Shanmugasundram (Genomics England Curator)

gene: TM2D3 was added gene: TM2D3 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: TM2D3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TM2D3 were set to 40449487 Phenotypes for gene: TM2D3 were set to Neurocardiorenal malformation syndrome, OMIM:621379 Review for gene: TM2D3 was set to GREEN