Monogenic diabetes

Gene: SMPD4

Green List (high evidence)

SMPD4 (sphingomyelin phosphodiesterase 4)
EnsemblGeneIds (GRCh38): ENSG00000136699
EnsemblGeneIds (GRCh37): ENSG00000136699
OMIM: 610457, Gene2Phenotype
SMPD4 is in 9 panels

2 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green and the mode of inheritance set to BIALLELIC, autosomal or pseudoautosomal following NHS Genomic Medicine Service approval.
Created: 5 Dec 2024, 7:05 p.m. | Last Modified: 5 Dec 2024, 7:05 p.m.
Panel Version: 2.60
Comment on list classification: As reviewed by Dmitrijs Rots, there are five individuals from three unrelated families with biallelic loss-of-function SMPD4 variants. They developed insulin-dependent diabetes, besides presenting with a severe neurodevelopmental disorder and microcephaly. In addition, review of past reports showed 27% of patients had insulin-dependent diabetes.

This gene can therefore be promoted to green rating in the next GMS review.
Created: 1 Mar 2024, 2:37 p.m. | Last Modified: 1 Mar 2024, 2:37 p.m.
Panel Version: 2.57

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies, OMIM:618622; type 1 diabetes mellitus, MONDO:0005147

Publications

Dmitrijs Rots (Children's Clinical University Hospital)

I don't know

PMID: 36732302 reported three independent families with multiple affected individuals with biallelic SMPD4 variants with severe NDD and insulin-dependent diabetes. Given the syndromic presentation - not sure about the relevancy for the panel.
Sources: Literature
Created: 10 Nov 2023, 4:45 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
NDD, microcephaly and diabetes

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
Phenotypes
  • Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies, OMIM:618622
  • type 1 diabetes mellitus, MONDO:0005147
OMIM
610457
Clinvar variants
Variants in SMPD4
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

5 Dec 2024, Gel status: 3

Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_24_promote_green was removed from gene: SMPD4.

5 Dec 2024, Gel status: 3

Added New Source, Added New Source, Status Update

Achchuthan Shanmugasundram (Genomics England Curator)

Source Expert Review Green was added to SMPD4. Source NHS GMS was added to SMPD4. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Mar 2024, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: smpd4 has been classified as Amber List (Moderate Evidence).

1 Mar 2024, Gel status: 0

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: SMPD4 were changed from NDD, microcephaly and diabetes to Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies, OMIM:618622; type 1 diabetes mellitus, MONDO:0005147

1 Mar 2024, Gel status: 0

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: SMPD4 were set to PMID: 36732302

1 Mar 2024, Gel status: 0

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_24_promote_green tag was added to gene: SMPD4.

10 Nov 2023, Gel status: 0

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

Dmitrijs Rots (Children's Clinical University Hospital)

gene: SMPD4 was added gene: SMPD4 was added to Monogenic diabetes. Sources: Literature Mode of inheritance for gene: SMPD4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SMPD4 were set to PMID: 36732302 Phenotypes for gene: SMPD4 were set to NDD, microcephaly and diabetes Penetrance for gene: SMPD4 were set to Complete Review for gene: SMPD4 was set to AMBER