LMAN2L

lectin, mannose binding 2 like

Basic information

Region (hg38): 2:96705929-96740064

Links

ENSG00000114988

∙ NCBI:81562 ∙ OMIM:609552 ∙ HGNC:19263 ∙ Uniprot:Q9H0V9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, autosomal recessive 52 (Limited), mode of inheritance: AR
autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
intellectual disability, autosomal recessive 52 (Limited), mode of inheritance: AR
intellectual developmental disorder, autosomal dominant 69 (Limited), mode of inheritance: AD
intellectual disability, autosomal recessive 52 (Limited), mode of inheritance: AR
complex neurodevelopmental disorder (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 69; Intellectual developmental disorder, autosomal recessive, 52	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	26566883; 31020005

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMAN2L gene.

not_specified (40 variants)
not_provided (15 variants)
Intellectual_disability,_autosomal_recessive_52 (9 variants)
LMAN2L-related_disorder (4 variants)
Neurodevelopmental_disorder (1 variants)
Hyperphosphatasia_with_intellectual_disability_syndrome_4 (1 variants)
Intellectual_developmental_disorder,_autosomal_dominant_69 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMAN2L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030805.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	11 clinvar		12
missense	1 clinvar	1 clinvar	41 clinvar	1 clinvar		44
nonsense						0
start loss						0
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	1	45	12	0

Highest pathogenic variant AF is 0.0000303604

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMAN2L	protein_coding	protein_coding	ENST00000377079	9	34136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-11	0.123	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.188	207	215	0.964	0.0000120	2329
Missense in Polyphen		79	88.665	0.89099		932
Synonymous	-0.235	86	83.3	1.03	0.00000433	706
Loss of Function	0.533	18	20.6	0.873	0.00000102	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000422	0.000421
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000440	0.000440
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be involved in the regulation of export from the endoplasmic reticulum of a subset of glycoproteins. May function as a regulator of ERGIC-53. {ECO:0000269|PubMed:12878160}.;
Pathway: Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

pRec: 0.127

Intolerance Scores

loftool: 0.820
rvis_EVS: -0.65
rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

pHI: 0.218
hipred: N
hipred_score: 0.282
ghis: 0.633

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.157

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Lman2l
Phenotype

Zebrafish Information Network

Gene name: lman2la
Affected structure: neuromast hair cell
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: protein folding;endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;Golgi organization;protein transport
Cellular component: Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;integral component of membrane;COPII-coated ER to Golgi transport vesicle
Molecular function: mannose binding;metal ion binding