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Intellectual disability

Gene: SPOUT1

Amber List (moderate evidence)
SPOUT1 (SPOUT domain containing methyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000198917
EnsemblGeneIds (GRCh37): ENSG00000198917
OMIM: 617614, Gene2Phenotype
SPOUT1 is in 5 panels

1 review

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Comment on publications: PMID: 39962046 was identified by the Genomics England Applied Machine Learning (ML) team in a Biocuration-ML project for identifying new gene-disease associations using Natural Language Processing (NLP) and Generative AI techniques.
Created: 17 Mar 2025, 1:47 p.m. | Last Modified: 17 Mar 2025, 1:47 p.m.
Panel Version: 8.146
PMID: 39962046 reports the association of biallelic SPOUT1 variants with SPOUT1 Associated Development delay Microcephaly Seizures Short stature. In this study, a total of 18 SPOUT1 variants were found in 28 individuals from 21 unrelated families. Intellectual disability was evident in 10/10 families where it could be ascertained, seizures were reported in 16/21 of the families and short stature was seen in 13/15 families where it could be measured.
SPOUT1 variant zebra fish models showed reduction in larval head size with concomitant apoptosis and the human SPOUT1 missense variants were pathogenic in complementation assays in zebrafish (PMID: 39962046).
Sources: Literature
Created: 17 Mar 2025, 1:43 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
SPOUT1 Associated Development delay Microcephaly Seizures Short stature

Publications

Created: 17 Mar 2025, 1:43 p.m.

Panel version: 8.144

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Neurodevelopmental disorder with poor growth, seizures, and brain abnormalities, OMIM:621154
Tags
Q1_25_ promote_green
OMIM
617614
Clinvar variants
Variants in SPOUT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

8 Sep 2025, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SPOUT1 were changed from SPOUT1 Associated Development delay Microcephaly Seizures Short stature to Neurodevelopmental disorder with poor growth, seizures, and brain abnormalities, OMIM:621154

17 Mar 2025, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SPOUT1 were set to 39962046

17 Mar 2025, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: spout1 has been classified as Amber List (Moderate Evidence).

17 Mar 2025, Gel status: 1

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

Sarah Leigh (Genomics England Curator)

gene: SPOUT1 was added gene: SPOUT1 was added to Intellectual disability. Sources: Literature Q1_25_ promote_green tags were added to gene: SPOUT1. Mode of inheritance for gene: SPOUT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SPOUT1 were set to 39962046 Phenotypes for gene: SPOUT1 were set to SPOUT1 Associated Development delay Microcephaly Seizures Short stature Review for gene: SPOUT1 was set to GREEN