LMAN1L

lectin, mannose binding 1 like

Basic information

Region (hg38): 15:74812715-74825757

Links

ENSG00000140506 ∙ NCBI:79748 ∙ OMIM:609548 ∙ HGNC:6632 ∙ Uniprot:Q9HAT1 ∙ 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 LMAN1L gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMAN1L 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			23	5		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	5	0

Variants in LMAN1L

This is a list of pathogenic ClinVar variants found in the LMAN1L region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74812862-C-T		not specified	Likely benign (Jul 13, 2021)
15-74812886-T-C		not specified	Uncertain significance (Jul 12, 2022)
15-74812901-T-G		not specified	Uncertain significance (Apr 26, 2023)
15-74812909-G-A		not specified	Uncertain significance (Jan 26, 2023)
15-74813002-G-A		not specified	Uncertain significance (Nov 06, 2023)
15-74816160-C-T		not specified	Uncertain significance (Apr 28, 2023)
15-74816166-T-A		not specified	Uncertain significance (Apr 28, 2023)
15-74816265-T-C		not specified	Uncertain significance (Feb 16, 2023)
15-74816280-C-T		not specified	Uncertain significance (Jul 17, 2023)
15-74816286-T-G		not specified	Uncertain significance (Mar 24, 2023)
15-74816467-T-C		not specified	Uncertain significance (Dec 16, 2023)
15-74816500-G-T		not specified	Uncertain significance (Jul 07, 2022)
15-74818734-G-A		not specified	Uncertain significance (Feb 13, 2024)
15-74818815-C-T		not specified	Uncertain significance (Nov 22, 2023)
15-74819233-G-A		not specified	Uncertain significance (Feb 13, 2024)
15-74819246-T-A		not specified	Uncertain significance (Dec 27, 2022)
15-74819251-G-A		not specified	Uncertain significance (Oct 25, 2022)
15-74820672-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-74820691-A-C		not specified	Uncertain significance (Jan 04, 2024)
15-74821102-C-T		not specified	Uncertain significance (Aug 02, 2022)
15-74821116-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-74821119-C-G		not specified	Uncertain significance (Dec 14, 2022)
15-74821137-C-T		not specified	Uncertain significance (Jul 25, 2023)
15-74821138-G-A		not specified	Likely benign (Nov 02, 2023)
15-74821164-G-A		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMAN1L	protein_coding	protein_coding	ENST00000309664	14	13043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-13	0.132	125274	1	473	125748	0.00189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.972	259	307	0.844	0.0000173	3333
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00129	0.00129
Ashkenazi Jewish	0.00	0.00
East Asian	0.000658	0.000653
Finnish	0.00206	0.00203
European (Non-Finnish)	0.00317	0.00313
Middle Eastern	0.000658	0.000653
South Asian	0.000471	0.000457
Other	0.00232	0.00228

dbNSFP

Source: dbNSFP

• 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: 0.0924

Intolerance Scores

• loftool: 0.916
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.83

Haploinsufficiency Scores

• pHI: 0.0508
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lman1l

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;Golgi organization
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment;integral component of membrane;COPII-coated ER to Golgi transport vesicle;endoplasmic reticulum-Golgi intermediate compartment membrane;collagen-containing extracellular matrix
• Molecular function: mannose binding