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Intellectual disability

Gene: DPH1

Green List (high evidence)
DPH1 (diphthamide biosynthesis 1)
EnsemblGeneIds (GRCh38): ENSG00000108963
EnsemblGeneIds (GRCh37): ENSG00000108963
OMIM: 603527, Gene2Phenotype
DPH1 is in 3 panels

2 reviews

Catherine Snow (Genomics England)

Comment on list classification: Expert review by Konstantinos Varvagiannis on DPH1. Overall there are 11 patients from 6 different families and DD/ID is a universal feature.

PMID 25558065, Alazami et al. identified 1 patient from the same consanguineous Saudi Arabian family (of 8 total similarly affected individuals) homozygous for the Leu234Pro (NM_001383.3:c.701T>C) variant.

PMID 26220823 Louks et al. report on 4 patients from 3 families belonging to the same genetic isolate from North America and provide details on 4 of the individuals identified by Alazami et al.

PMIDs 29362492 and 29410513 report on 3 further patients with similar (as well as some additional) features including DD/ID. The individual in the first article was compound heterozygous for a missense (Leu164Pro) and a frameshift variant (c.289delG) while 2 sibs born to consanguineous parents in the second article were homozygous for a frameshift variant (c.1227delG).

Associated with relevant phenotype in OMIM - "Developmental delay with short stature, dysmorphic features, and sparse hair", but no entry currently in G2P.

There are sufficient cases of ID/DD from unrelated families to warrant a Green rating.
Created: 20 May 2019, 12:24 p.m. | Last Modified: 17 Jul 2019, 10:36 a.m.
Panel Version: 0.200
Created: 20 May 2019, 12:24 p.m.
Last Modified: 17 Jul 2019, 10:36 a.m.
Panel version: Imported from Intellectual disability update May 2019 panel version 0.31

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Biallelic mutations in DPH1 cause Developmental delay with short stature, dysmorphic features, and sparse hair, MIM 616901.

Overall 11 patients from 6 different families have probably been reported in detail. DD/ID is a universal feature.

In PMID 25558065, Alazami et al. identified 1 patient from the same consanguineous Saudi Arabian family (of 8 total similarly affected individuals) homozygous for the Leu234Pro (NM_001383.3:c.701T>C) variant. This individual was part of a large cohort of patients with neurogenetic disorders from consanguineous families. The phenotype is not described in detail.

In PMID 26220823 Louks et al. report on 4 patients from 3 families belonging to the same genetic isolate from North America and provide details on 4 of the individuals identified by Alazami et al.

The individuals identified in this study were homozygous for Met6Lys which was however predicted to be benign and tolerated (by PolyPhen2 and SIFT respectively) in silico.

DD/ID, unusual skull shape, ectodermal anomalies were universal (8/8) with additional features including short stature (7/8), renal (4/6) or cardiac anomalies (3/8). Some facial features appeared to be common, too.

Functional studies were not performed. However Dph1 pathogenic variants in mice result in restricted growth, craniofacial and developmental defects similar to the human phenotypes (PMIDs 14744934 and 24895408 are cited).

PMIDs 29362492 and 29410513 report on 3 further patients with similar (as well as some additional) features including DD/ID. The individual in the first article was compound heterozygous for a missense (Leu164Pro) and a frameshift variant (c.289delG) while 2 sibs born to consanguineous parents in the second article were homozygous for a frameshift variant (c.1227delG).

The phenotype appears to be consistent among all the published patients.

DPH1 is included in gene panels for intellectual disability offered by different diagnostic laboratories.

As a result, this gene can be considered for inclusion in this panel as green.
Sources: Literature
Created: 26 Nov 2018, 5:03 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Developmental delay with short stature, dysmorphic features, and sparse hair, 616901

Publications

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

Created: 26 Nov 2018, 5:03 p.m.

Panel version: 2.556

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Expert Review
Phenotypes
  • Developmental delay with short stature, dysmorphic facial features, and sparse hair, OMIM:616901
OMIM
603527
Clinvar variants
Variants in DPH1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

2 Jun 2021, Gel status: 3

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: DPH1 were set to 29362492; 29410513; 26220823; 25558065

2 Jun 2021, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: DPH1 were changed from Developmental delay with short stature, dysmorphic features, and sparse hair, 616901 to Developmental delay with short stature, dysmorphic facial features, and sparse hair, OMIM:616901

25 Jul 2019, Gel status: 3

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

Catherine Snow (Genomics England)

Source Expert Review Green was added to DPH1. Added phenotypes Developmental delay with short stature, dysmorphic features, and sparse hair, 616901 for gene: DPH1 Publications for gene DPH1 were changed from 25558065; 26220823; 29362492; 29410513 to 29362492; 29410513; 26220823; 25558065 Rating Changed from No List (delete) to Green List (high evidence)

26 Nov 2018, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: DPH1 was added gene: DPH1 was added to Intellectual disability. Sources: Literature,Expert Review Mode of inheritance for gene: DPH1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DPH1 were set to 25558065; 26220823; 29362492; 29410513 Phenotypes for gene: DPH1 were set to Developmental delay with short stature, dysmorphic features, and sparse hair, 616901 Penetrance for gene: DPH1 were set to Complete Review for gene: DPH1 was set to GREEN gene: DPH1 was marked as current diagnostic