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Intellectual disability

Gene: LDB1

Amber List (moderate evidence)
LDB1 (LIM domain binding 1)
EnsemblGeneIds (GRCh38): ENSG00000198728
EnsemblGeneIds (GRCh37): ENSG00000198728
OMIM: 603451, Gene2Phenotype
LDB1 is in 3 panels

1 review

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.

Although ventriculomegaly and/or hydrocephalus are the primary feature of the disorder, at least seven unrelated individuals have been reported with GDD and several also exhibited hypotonia. Taking this into account and the broader syndromic presentation, it would be appropriate to include this gene on the R27 Paediatric disorders and R69 Hypotonic infant super panels, both of which incorporate Intellectual disability as a component panel.
Created: 12 Dec 2025, 11:43 a.m. | Last Modified: 12 Dec 2025, 11:43 a.m.
Panel Version: 9.194
- Allington et al. 2024 (PMID: 39680505) investigate a cohort of 2697 trios with congenital primary cerebral ventriculomegaly using WES. Eight unrelated individuals identified with de novo variants in LDB1 (7 LOF, 1 predicted damaging missense) - exhibiting perinatally diagnosed cerebral ventriculomegaly, including neurosurgically treated congenital hydrocephalus. Additionally, 5/8 GDD, 3/8 autism, 2/8 delayed gross motor development, 2/8 had congenital heart defects (inc. coarctation, PDA), 2/8 camptodactyly.

Additional case was identified from GeneMatcher with a de novo frameshift variants in LDB1. Phenotypes include severe ventriculomegaly, absence of well formed gyri, severe limb contractures and camptodactyly. Search of Decipher/DDD also revealed 4 pathogenic de novo variants in LDB1 and associated binding partners in individuals congenital ventriculomegaly.

- Torene et al. 2023 (PMID: 38091987) identified three individuals with protein truncating variants. Two individuals with de novo variants both had ventriculomegaly, hypotonia, GDD, craniofacial abnormalities. The third individual inherited the variants from an asymptomatic mother, and displayed developmental delay, hypotonia, congenital heart defects and a small hypoplastic hippocampi but did not have ventriculomegaly or craniofacial anomalies.

- Jin et al. 2020 (PMID: 33077954) also report an individual with a de novo LOF variant in this gene who had congenital hydrocephalus but details on this case are otherwise limited.
Sources: Literature
Created: 12 Dec 2025, 11:32 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Congenital hydrocephalus, MONDO:0016349

Publications

Created: 12 Dec 2025, 11:32 a.m.

Panel version: 9.193

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Congenital hydrocephalus, MONDO:0016349
Tags
Q4_25_promote_green gene-checked
OMIM
603451
Clinvar variants
Variants in LDB1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

19 Dec 2025, Gel status: 2

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag gene-checked tag was added to gene: LDB1.

12 Dec 2025, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: ldb1 has been classified as Amber List (Moderate Evidence).

12 Dec 2025, Gel status: 1

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

Arina Puzriakova (Genomics England Curator)

gene: LDB1 was added gene: LDB1 was added to Intellectual disability. Sources: Literature Q4_25_promote_green tags were added to gene: LDB1. Mode of inheritance for gene: LDB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: LDB1 were set to 39680505; 38091987; 33077954 Phenotypes for gene: LDB1 were set to Congenital hydrocephalus, MONDO:0016349 Review for gene: LDB1 was set to GREEN