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Intellectual disability

Gene: LSM1

Amber List (moderate evidence)
LSM1 (LSM1 homolog, mRNA degradation associated)
EnsemblGeneIds (GRCh38): ENSG00000175324
EnsemblGeneIds (GRCh37): ENSG00000175324
OMIM: 607281, Gene2Phenotype
LSM1 is in 1 panel

1 review

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are six unrelated families reported with biallelic LSM 1 variants (c.231+4A>C in five families and p.Asn40Tyr in one family) and with FICUS syndrome (which includes global developmental delay/ intellectual disability). Hence, this gene can be promoted to green rating in the next GMS update.
Created: 6 Jan 2026, 2:39 p.m. | Last Modified: 6 Jan 2026, 2:39 p.m.
Panel Version: 9.224
PMID:31010896 (2019) reported two siblings with global developmental delay, and multiple congenital anomalies affecting the cardiac, genitourinary, and skeletal systems, and abnormal eye movements. They were identified with a homozygous non-canonical splice variant in LSM1 gene (c.231+4A>C) through whole-genome sequencing. There is also functional evidence available from expression studies and mouse model. Lsm1 knockout mice had a partially overlapping phenotype that affected the brain, heart, and eye.

PMID:36100156 (2022) reported the identification of a homozygous missense variant (p.Asn40Tyr) in LSM1 gene via whole-exome in two similarly affected siblings with global neurodevelopmental delay and intellectual disability.

PMID:40204357 (2025) reported six paediatric patients from four unrelated families with homozygous c.231+4A>C variant. They presented with dysmorphic facial features, global developmental delay/ intellectual disability and multisystemic involvement, including urological, cardiac and skeletal manifestations. This variant was identified in Muslim Arab and Ashkenazi Jewish populations and determined as representing a hotspot variant through haplotype analysis. RT-qPCR functional validation demonstrated exon 3 skipping and elevated mutant isoform. The variant was classified as 'Pathogenic' according to the ACMG classification.

This gene has been associated with relevant phenotypes in OMIM (MIM #621193, OMIM record last accessed 06 January 2026), but not yet in Gene2Phenotype.
Sources: Literature
Created: 6 Jan 2026, 2:35 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
FICUS syndrome, OMIM:621193; FICUS syndrome, MONDO:0978296

Publications

Created: 6 Jan 2026, 2:35 p.m.

Panel version: 9.223

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • FICUS syndrome, OMIM:621193
  • FICUS syndrome, MONDO:0978296
Tags
Q1_26_promote_green
OMIM
607281
Clinvar variants
Variants in LSM1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

6 Jan 2026, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: lsm1 has been classified as Amber List (Moderate Evidence).

6 Jan 2026, Gel status: 1

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q1_26_promote_green tag was added to gene: LSM1.

6 Jan 2026, Gel status: 1

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

Achchuthan Shanmugasundram (Genomics England Curator)

gene: LSM1 was added gene: LSM1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: LSM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LSM1 were set to 31010896; 36100156; 40204357 Phenotypes for gene: LSM1 were set to FICUS syndrome, OMIM:621193; FICUS syndrome, MONDO:0978296 Review for gene: LSM1 was set to GREEN