LAMP1

lysosomal associated membrane protein 1, the group of Lysosome associated membrane proteins|CD molecules

Basic information

Region (hg38): 13:113297239-113323672

Links

ENSG00000185896 ∙ NCBI:3916 ∙ OMIM:153330 ∙ HGNC:6499 ∙ Uniprot:P11279 ∙ 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 LAMP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMP1 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				1	3	4
missense			28	2	3	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	3	6

Variants in LAMP1

This is a list of pathogenic ClinVar variants found in the LAMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113297444-C-T		not specified	Uncertain significance (Apr 24, 2024)
13-113297456-C-G		not specified	Uncertain significance (Jan 26, 2022)
13-113297487-T-C		not specified	Uncertain significance (Jul 13, 2021)
13-113306497-G-A		not specified	Uncertain significance (Aug 02, 2022)
13-113306498-T-G		not specified	Uncertain significance (Feb 28, 2024)
13-113306517-A-G		not specified	Likely benign (May 03, 2023)
13-113306530-G-A			Benign (Mar 30, 2018)
13-113309653-T-C		not specified	Uncertain significance (Jul 14, 2023)
13-113309683-T-C			Benign (Jun 08, 2018)
13-113309796-G-A		not specified	Uncertain significance (Feb 12, 2024)
13-113309817-T-G		not specified	Uncertain significance (May 24, 2024)
13-113309838-C-G			Benign (Dec 31, 2019)
13-113309848-A-G		not specified	Uncertain significance (Nov 04, 2023)
13-113309848-A-T		not specified	Uncertain significance (Jun 02, 2023)
13-113309856-T-C		not specified	Uncertain significance (Oct 13, 2023)
13-113310751-T-C		not specified	Uncertain significance (Sep 06, 2022)
13-113310796-A-G		not specified	Uncertain significance (Sep 17, 2021)
13-113310807-G-A		not specified	Uncertain significance (Oct 03, 2022)
13-113310838-A-G		not specified	Uncertain significance (Mar 01, 2023)
13-113310851-C-G		not specified	Uncertain significance (Jan 16, 2024)
13-113310871-G-A			Benign (Mar 30, 2018)
13-113319488-C-A		not specified	Uncertain significance (Jul 13, 2021)
13-113319507-G-A		not specified	Uncertain significance (May 09, 2024)
13-113319546-C-T		not specified	Uncertain significance (Mar 29, 2023)
13-113319558-T-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMP1	protein_coding	protein_coding	ENST00000332556	9	26432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.875	0.125	124401	6	675	125082	0.00273

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.829	220	257	0.855	0.0000158	2708
Missense in Polyphen		52	75.477	0.68895		902
Synonymous	-0.501	120	113	1.06	0.00000832	862
Loss of Function	3.19	2	15.6	0.128	7.41e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000579	0.000571
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000798	0.000785
Middle Eastern	0.000167	0.000167
South Asian	0.0186	0.0186
Other	0.00183	0.00180

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Presents carbohydrate ligands to selectins. Also implicated in tumor cell metastasis.
• Pathway: Phagosome - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Lysosome - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Senescence and Autophagy in Cancer;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.792

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.169
• hipred: Y
• hipred_score: 0.514
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lamp1
• Phenotype: craniofacial phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: granzyme-mediated apoptotic signaling pathway;neutrophil degranulation;positive regulation of natural killer cell degranulation;positive regulation of natural killer cell mediated cytotoxicity;viral entry into host cell;autophagic cell death;protein stabilization;establishment of protein localization to organelle;Golgi to lysosome transport;regulation of organelle transport along microtubule
• Cellular component: cytoplasm;lysosome;lysosomal membrane;late endosome;multivesicular body;cytosol;plasma membrane;integral component of plasma membrane;external side of plasma membrane;endosome membrane;membrane;integral component of synaptic vesicle membrane;dendrite;azurophil granule membrane;sarcolemma;melanosome;neuronal cell body;cytolytic granule;autolysosome;perinuclear region of cytoplasm;phagolysosome membrane;extracellular exosome;alveolar lamellar body;ficolin-1-rich granule membrane
• Molecular function: virus receptor activity;protein binding;enzyme binding;protein domain specific binding