LMAN2

lectin, mannose binding 2

Basic information

Region (hg38): 5:177315805-177351840

Previous symbols: [ "C5orf8" ]

Links

ENSG00000169223 ∙ NCBI:10960 ∙ OMIM:609551 ∙ HGNC:16986 ∙ Uniprot:Q12907 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMAN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMAN2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			20	1	2	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	2

Variants in LMAN2

This is a list of pathogenic ClinVar variants found in the LMAN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-177332142-C-G		not specified	Uncertain significance (Dec 20, 2023)
5-177332169-C-T			Benign (Sep 29, 2018)
5-177332201-G-A		not specified	Uncertain significance (Feb 17, 2022)
5-177334289-G-C		not specified	Uncertain significance (Dec 19, 2023)
5-177334361-A-G		not specified	Uncertain significance (Jan 06, 2023)
5-177334381-C-A		not specified	Uncertain significance (Aug 30, 2022)
5-177337174-T-C		not specified	Uncertain significance (Mar 15, 2024)
5-177337373-C-T		not specified	Uncertain significance (May 24, 2024)
5-177337386-G-A		not specified	Uncertain significance (Jan 22, 2024)
5-177337395-G-C		not specified	Uncertain significance (Mar 01, 2024)
5-177337413-G-A		not specified	Uncertain significance (Dec 01, 2022)
5-177337418-C-T		not specified	Uncertain significance (Feb 13, 2024)
5-177337523-C-T		not specified	Uncertain significance (Feb 15, 2023)
5-177337737-A-G		not specified	Uncertain significance (Aug 17, 2022)
5-177337783-G-T		not specified	Uncertain significance (Feb 16, 2023)
5-177338521-C-T		not specified	Uncertain significance (Aug 17, 2022)
5-177338557-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-177351255-T-C		not specified	Uncertain significance (Mar 04, 2024)
5-177351261-T-G		not specified	Uncertain significance (Nov 10, 2022)
5-177351532-A-G			Benign (Sep 19, 2018)
5-177351551-G-A		not specified	Uncertain significance (Jan 20, 2023)
5-177351581-G-C		not specified	Uncertain significance (Oct 16, 2023)
5-177351612-C-G		not specified	Uncertain significance (Jan 06, 2023)
5-177351614-A-T		not specified	Uncertain significance (Aug 22, 2023)
5-177351622-C-A		not specified	Likely benign (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMAN2	protein_coding	protein_coding	ENST00000303127	8	20291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000107	0.952	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.382	234	251	0.932	0.0000170	2336
Missense in Polyphen		95	124.39	0.76373		1126
Synonymous	-1.09	125	110	1.13	0.00000834	706
Loss of Function	1.79	9	16.9	0.532	7.26e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000806	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000981	0.0000980
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as an intracellular lectin in the early secretory pathway. Interacts with N-acetyl-D-galactosamine and high-mannose type glycans and may also bind to O-linked glycans. Involved in the transport and sorting of glycoproteins carrying high mannose-type glycans (By similarity). {ECO:0000250}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);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: 0.142

Intolerance Scores

• loftool: 0.506
• rvis_EVS: -0.75
• rvis_percentile_EVS: 13.58

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.329
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lman2

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;endoplasmic reticulum organization;Golgi organization;protein transport;positive regulation of phagocytosis
• Cellular component: Golgi membrane;extracellular space;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;integral component of plasma membrane;cell surface;COPII-coated ER to Golgi transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;extracellular exosome
• Molecular function: protein binding;mannose binding;carbohydrate binding;heat shock protein binding;metal ion binding