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DDG2P

Gene: TSPAN7

Green List (high evidence)
TSPAN7 (tetraspanin 7)
EnsemblGeneIds (GRCh38): ENSG00000156298
EnsemblGeneIds (GRCh37): ENSG00000156298
OMIM: 300096, Gene2Phenotype
TSPAN7 is in 3 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Comment on list classification: There are at least 7 unrelated individuals reported with mild to moderate intellectual disability with either LoF variants in TSPAN7, TSPAN7 duplication, or balanced translocations with a breakpoint within the TSPAN7 sequence. However, phenotype in most of the affected individuals does not meet the eligibility criteria of moderate/severe/profound global developmental delay/intellectual disability. There is also conflicting evidence for pathogenicity of the reported variants, including high population allele frequencies, predicted NMD escape, and sequencing method limitations. Based on the available evidence, we decided to demote this gene to Amber for Intellectual disability.
Created: 30 Sep 2025, 2:35 p.m. | Last Modified: 30 Sep 2025, 2:35 p.m.
Panel Version: 6.5

Mode of inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females

Phenotypes
Intellectual developmental disorder, X-linked 58, OMIM:300210; intellectual disability, MONDO:0001071

Publications

Created: 30 Sep 2025, 2:35 p.m.
Last Modified: 30 Sep 2025, 2:35 p.m.
Panel version: 6.5

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The DDG2P confidence category for the disease INTELLECTUAL DEVELOPMENTAL DISORDER X-LINKED TYPE 58, OMIM:300210 is definitive. The allelic requirement and mutation consequence are monoallelic_X_hem and absent gene product (PMIDs: 10449641;10655063).
Created: 4 Oct 2023, 5:08 p.m. | Last Modified: 4 Oct 2023, 5:08 p.m.
Panel Version: 3.12

Mode of inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females

Phenotypes
INTELLECTUAL DEVELOPMENTAL DISORDER X-LINKED TYPE 58, OMIM:300210

Publications

Created: 4 Oct 2023, 5:08 p.m.
Last Modified: 4 Oct 2023, 5:08 p.m.
Panel version: 3.12

Rebecca Foulger (Genomics England curator)

I don't know

Original DDG2P rating: confirmed.
Created: 19 Nov 2018, 11:31 a.m.
Created: 19 Nov 2018, 11:31 a.m.

Panel version: 0.2

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, biallelic mutations in females
Sources
  • DD-Gene2Phenotype
  • Expert Review Green
Phenotypes
  • MENTAL RETARDATION X-LINKED TYPE 58 300210
OMIM
300096
Clinvar variants
Variants in TSPAN7
Penetrance
None
Publications
Panels with this gene

History Filter Activity

4 Oct 2023, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: TSPAN7 were updated from 10449641; 10655063 to 10655063; 10449641

29 Jan 2019, Gel status: 4

Panel promoted to version 1.0

Rebecca Foulger (Genomics England curator)

Rebecca Foulger: Original DDG2P rating: confirm

19 Nov 2018, Gel status: 4

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

Rebecca Foulger (Genomics England curator)

gene: TSPAN7 was added gene: TSPAN7 was added to DDG2P. Sources: Expert Review Green,DD-Gene2Phenotype Mode of inheritance for gene: TSPAN7 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: TSPAN7 were set to 10449641; 10655063 Phenotypes for gene: TSPAN7 were set to MENTAL RETARDATION X-LINKED TYPE 58 300210