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Intellectual disability

Gene: LMAN2L

Amber List (moderate evidence)
LMAN2L (lectin, mannose binding 2 like)
EnsemblGeneIds (GRCh38): ENSG00000114988
EnsemblGeneIds (GRCh37): ENSG00000114988
OMIM: 609552, Gene2Phenotype
LMAN2L is in 2 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on phenotypes: OMIM phenotype updated 13th Aug 2026.
Created: 13 Aug 2026, 11:41 a.m. | Last Modified: 13 Aug 2026, 11:41 a.m.
Panel Version: 11.7
There are now 3 unrelated probands reported in literature with biallelic LMAN2L variants and severe GDD/ID. There is also one pedigree reported with a heterozygous LMAN2L variant segregating with ID. Hence, this gene can be promoted to Green at the next update, with MOI set to 'BIALLELIC, autosomal or pseudoautosomal', until more evidence emerges for the dominant association.
Created: 13 Aug 2026, 11:37 a.m. | Last Modified: 13 Aug 2026, 11:37 a.m.
Panel Version: 11.4
PMID: 40221759 Wang et al. 2025
Report of 2 sibs with LMAN2L compound heterozygous variants, c.476A>G, p.D159G and c.1060_1061del, p.S354Pfs*29. Some family history of epilepsy (parents' cousins) but no ID history. Parents are not related.
Proband (Case 1, female) had intellectual disability, severe developmental delays, and epileptic seizures at the age of 2 months. The child has a low immunity and is hospitalized for severe pneumonia about 4–5 times a year. She also had developmental dysplasia of the hip and low muscle tone.
Case 2 - male, hospitalised for feeding difficulties; bilateral hearing impariment noted; he had edema, low muscle tone, and an umbilical hernia. Developed tonic clonic seizures at 2 months.
Epilepsy was resistant to medication in both sibs.

PMID: 37667433 Zhou et al., 2023
Report of a Chinese female proband, 3yo, from a non-consanguineous family with comp het LMAN2L variants: c.902del (p.F301Sfs∗8) and c.256C>T (p.R86C). Method: Trio WES. Patient was diagnosed with general growth retardation, epilepsy (tonic seizures with onset at 2 months), and hearing loss. She showed a general developmental delay. She had difficulty in sitting, standing, walking, speaking, and making social interactions. Hypotonia was also noted. Parents, het carriers for a variant each, were unaffected.
Created: 13 Aug 2026, 11:35 a.m. | Last Modified: 13 Aug 2026, 11:35 a.m.
Panel Version: 11.4

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
?Intellectual developmental disorder, autosomal dominant 69, OMIM:617863; ?Intellectual developmental disorder, autosomal recessive 52, OMIM:616887

Publications

Created: 13 Aug 2026, 11:35 a.m.
Last Modified: 13 Aug 2026, 11:35 a.m.
Panel version: 11.4

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Two families with ID phenotype (one mild, one severe). Amber rating as additional cases and functional data are required to validate the causal association with the phenotype.
Created: 31 Jul 2020, 10:06 a.m. | Last Modified: 31 Jul 2020, 10:06 a.m.
Panel Version: 3.211
Created: 31 Jul 2020, 10:06 a.m.
Last Modified: 31 Jul 2020, 10:06 a.m.
Panel version: 3.211

Zornitza Stark (Australian Genomics)

I don't know

1 consanguineous family with 7 individuals with ID and epilepsy, with homozygous LMAN2L missense mutation. Segregated with disease in family, and unaffected family members were heterozygous variant carriers. No functional studies.

1 non-consanguineous family with 4 affected with heterozygous frameshift LMAN2L mutation. Segregates in family. Mutation eliminates LMAN2L's endoplasmic reticulum retention signal and mislocalizes the protein from that compartment to the plasma membrane.

Amber or Red.
Sources: Expert list
Created: 9 Feb 2020, 7:08 a.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Intellectual disability; epilepsy

Publications

Created: 9 Feb 2020, 7:08 a.m.

Panel version: 3.0

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • ?Intellectual developmental disorder, autosomal dominant 69, OMIM:617863
  • ?Intellectual developmental disorder, autosomal recessive 52, OMIM:61688
  • intellectual disability, autosomal recessive 52, MONDO:0014815
  • intellectual developmental disorder, autosomal dominant 69, MONDO:0029465
Tags
Q3_26_promote_green
OMIM
609552
Clinvar variants
Variants in LMAN2L
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Aug 2026, Gel status: 2

Removed Tag, Added Tag

Ida Ertmanska (Genomics England Curator)

Tag watchlist was removed from gene: LMAN2L. Tag Q3_26_promote_green tag was added to gene: LMAN2L.

13 Aug 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: LMAN2L were changed from Intellectual disability; epilepsy to ?Intellectual developmental disorder, autosomal dominant 69, OMIM:617863; ?Intellectual developmental disorder, autosomal recessive 52, OMIM:61688; intellectual disability, autosomal recessive 52, MONDO:0014815; intellectual developmental disorder, autosomal dominant 69, MONDO:0029465

13 Aug 2026, Gel status: 2

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: LMAN2L were set to 31020005; 26566883

13 Aug 2026, Gel status: 2

Set mode of inheritance

Ida Ertmanska (Genomics England Curator)

Mode of inheritance for gene: LMAN2L was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

31 Jul 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: lman2l has been classified as Amber List (Moderate Evidence).

31 Jul 2020, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist tag was added to gene: LMAN2L.

9 Feb 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: LMAN2L was added gene: LMAN2L was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: LMAN2L was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: LMAN2L were set to 31020005; 26566883 Phenotypes for gene: LMAN2L were set to Intellectual disability; epilepsy Review for gene: LMAN2L was set to AMBER