LMAN1L

protein-coding

lectin, mannose binding 1 like

Gene summary

This gene encodes a mannose-binding type 1 transmembrane protein that contains an N-terminal lectin-like carbohydrate recognition domain. The encoded protein is similar in structure to lectins found in leguminous plants. This lectin is thought to transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment. [provided by RefSeq, Jan 2017]

MANE transcript

NM_021819.3

Inheritance

—

ClinVar variants

U:76B:10

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr15:74,812,716-74,825,757

External References & Databases

Ensembl (ENSG00000140506)

Transcript & Mutation Effects

hg38 • Region Span ~13.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LMAN1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

Prostate cancerTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021819.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			76 clinvar	10 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	10	0	86

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021819.3	RefSeq	NP_068591.2	14	MANE Select
ENST00000309664.10	Ensembl	ENSP00000310431.5	14	MANE Select
ENST00000379709.7	Ensembl	ENSP00000369031.3	13	Standard
ENST00000379709.8	Ensembl	ENSP00000369031.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein processing in endoplasmic reticulum - Homo sapiens (human)
Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
endoplasmic reticulum organization
Golgi organization

Molecular Function

mannose binding

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
endoplasmic reticulum-Golgi intermediate compartment
integral component of membrane
COPII-coated ER to Golgi transport vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309664
Coding exons: 14
Length: 13043
Individuals with no LoFs: 125274
Homozygous LoFs: 1
Heterozygous LoFs: 473
Defined: 125748
p: 0.00189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.972	259	307	0.844	0.0000173	3333
Missense (PolyPhen)		53	80.303	0.66		1006
Synonymous	0.674	117	127	0.924	0.00000712	1129
Loss of Function	0.810	22	26.5	0.830	0.00000120	282

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00080	0.00078	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00066	0.00065	rare
Finnish	0.0021	0.0020	notable
European (Non-Finnish)	0.0032	0.0031	notable
South Asian	0.00047	0.00046	rare
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0924

Intolerance Scores

LoFtool: 0.916
RVIS EVS: 0.93
RVIS percentile EVS: 89.83

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.124

Gene Damage Prediction

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