Intellectual disability
Gene: PTPMT1

PTPMT1 (protein tyrosine phosphatase, mitochondrial 1)
EnsemblGeneIds (GRCh38): ENSG00000110536
EnsemblGeneIds (GRCh37): ENSG00000110536
OMIM: 609538, Gene2Phenotype
PTPMT1 is in 6 panels

1 review

Arina Puzriakova (Genomics England Curator)

I don't know

New gene-disease association. Currently not associated with any phenotype in OMIM or G2P.

PMID:39279645 (2025) - 6 individuals from 3 unrelated families identified with biallelic variants in this gene. All patients presented with a complex, neonatal/infantile onset neurological and neurodevelopmental syndrome, however there was variability in the overall clinical presentation between families. Features include developmental delay, microcephaly, facial dysmorphism, epilepsy, spasticity, cerebellar ataxia and nystagmus, sensorineural hearing loss, optic atrophy and bulbar dysfunction. Brain MRI revealed a variable combination of corpus callosum thinning, cerebellar atrophy and white matter changes.

Patient from Family 1 harboured a homozygous missense variant (c.65A>C) while Family 2 and 3 carried the same homozygous variant (c.255G>C) and were shown to share some common ancestry using DNA microarray analysis.

Knockout zebrafish model displayed abnormalities in body size, developmental alterations, decreased total cardiolipin levels and OXPHOS deficiency.

Overall can be classified as Amber on the basis that two families were shown to be distantly related and no specific features were observed universally across all cases (GDD was mild in 5/6 individuals so outside the scope of the ID panel).
Sources: Literature
Created: 12 Mar 2025, 3:59 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
neurodevelopmental disorder, MONDO:0700092

Publications

39279645

Created: 12 Mar 2025, 3:59 p.m.

Panel version: 8.135

Details

Mode of Inheritance

BIALLELIC, autosomal or pseudoautosomal

Sources

Literature

Phenotypes

neurodevelopmental disorder, MONDO:0700092

Tags

watchlist

OMIM

609538

Clinvar variants

Variants in PTPMT1

Penetrance

None

Publications

39279645

Panels with this gene

History Filter Activity

12 Mar 2025, Gel status: 1

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

Arina Puzriakova (Genomics England Curator)

gene: PTPMT1 was added gene: PTPMT1 was added to Intellectual disability. Sources: Literature watchlist tags were added to gene: PTPMT1. Mode of inheritance for gene: PTPMT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PTPMT1 were set to 39279645 Phenotypes for gene: PTPMT1 were set to neurodevelopmental disorder, MONDO:0700092 Review for gene: PTPMT1 was set to AMBER

Intellectual disability Gene: PTPMT1