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  3. PITRM1
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Intellectual disability

Gene: PITRM1

Green List (high evidence)
PITRM1 (pitrilysin metallopeptidase 1)
EnsemblGeneIds (GRCh38): ENSG00000107959
EnsemblGeneIds (GRCh37): ENSG00000107959
PITRM1 is in 5 panels

2 reviews

Catherine Snow (Genomics England)

Comment on list classification: PITRM1 identified by expert review by Konstantinos Varvagiannis. Currently no OMIM or G2P terms association. PMID: 29764912 reports on 2 consanguineous Palestinian families each with 2 affected boys. Both Palenstinian families are from Arab descent but are from different locale. PMID: 26697887 reports 2 siblings from a consanguineous Norwegian family homozygous for a missense variant (NM_014889.2:c.548G> or p.Arg183Gln). Although there is some functional work (PMID: 29383861) phenotypes are varied in severity. However sufficient unrelated families (>3) for PITRM1 to be classified as Green.
Created: 29 May 2019, 9:45 a.m.
Created: 29 May 2019, 9:45 a.m.

Panel version: Imported from Intellectual disability update May 2019 panel version 0.95

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Biallelic pathogenic variants in PITRM1 seem to be associated with a phenotype of DD/ID and spinocerebellar ataxia.

6 individuals from 3 unrelated families have been reported.

PMID: 26697887 reports on 2 individuals from a consanguineous Norwegian family homozygous for a missense variant (NM_014889.2:c.548G> or p.Arg183Gln).

PMID: 29764912 reports on 2 consanguineous Palestinian families each with 2 affected boys. All affected individuals for both families were homozygous for a further missense variant (p.Thr931Met).

The boys from one Palestinian family appeared to be more severely affected - compared to the sibs from the other family with the same variant - due to a concurrent X-chromosome rearrangement.

Pathogenicity is supported by extensive functional studies performed in both articles as well as an additional one (PMID: 29383861) on Arg183Gln.

PITRM1 is included in gene panels for ID offered by (few) diagnostic laboratories.

The gene is not associated with any phenotype in OMIM nor in G2P.

As a result, PITRM1 can be considered for inclusion in the ID panel as green (or amber).
Sources: Literature
Created: 14 Dec 2018, 2:51 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Intellectual disability; Ataxia

Publications

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

Created: 14 Dec 2018, 2:51 p.m.

Panel version: 2.584

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review
  • Expert Review Green
  • Expert Review Green
  • Expert Review
Phenotypes
  • Spinocerebellar ataxia, autosomal recessive 30, OMIM:619405
Tags
gene-checked
Clinvar variants
Variants in PITRM1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

8 May 2022, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: PITRM1.

24 Sep 2021, Gel status: 3

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: PITRM1 were changed from Ataxia; Intellectual disability to Spinocerebellar ataxia, autosomal recessive 30, OMIM:619405

25 Jul 2019, Gel status: 3

Added New Source, Added New Source, Set Phenotypes, Status Update

Catherine Snow (Genomics England)

Source Expert Review Green was added to PITRM1. Source Expert Review was added to PITRM1. Added phenotypes Ataxia; Intellectual disability for gene: PITRM1 Rating Changed from No List (delete) to Green List (high evidence)

14 Dec 2018, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: PITRM1 was added gene: PITRM1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: PITRM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PITRM1 were set to 26697887; 29764912; 29383861 Phenotypes for gene: PITRM1 were set to Intellectual disability; Ataxia Penetrance for gene: PITRM1 were set to Complete Review for gene: PITRM1 was set to GREEN gene: PITRM1 was marked as current diagnostic