LAMP1

protein-coding

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

Gene summary

The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may also play a role in tumor cell metastasis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005561.4

Inheritance

—

ClinVar variants

U:65B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr13:113,297,239-113,323,672

External References & Databases

Ensembl (ENSG00000185896)

Transcript & Mutation Effects

hg38 • Region Span ~26.4 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 LAMP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 68

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005561.4. 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			1 clinvar	3 clinvar	2 clinvar	6
missense			61 clinvar	3 clinvar	3 clinvar	67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	65	6	5	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005561.4	RefSeq	NP_005552.3	9	MANE Select
ENST00000332556.5	Ensembl	ENSP00000333298.4	9	MANE Select
ENST00000886113.1	Ensembl	ENSP00000556172.1	6	Standard
ENST00000886113.2	Ensembl	ENSP00000556172.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Phagosome - Homo sapiens (human)
Autophagy - animal - Homo sapiens (human)
Lysosome - Homo sapiens (human)
Tuberculosis - Homo sapiens (human)
Senescence and Autophagy in Cancer

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

Molecular Function

virus receptor activity
protein binding
enzyme binding
protein domain specific binding

Cellular Component

cytoplasm
lysosome
lysosomal membrane
late endosome
multivesicular body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332556
Coding exons: 9
Length: 26432
Individuals with no LoFs: 124401
Homozygous LoFs: 6
Heterozygous LoFs: 675
Defined: 125082
p: 0.00273

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.829	220	257	0.855	0.0000158	2708
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00032	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00080	0.00078	rare
South Asian	0.019	0.019	notable
Other	0.0018	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Presents carbohydrate ligands to selectins. Also implicated in tumor cell metastasis.;

Recessive Scores

pRec: 0.792

Intolerance Scores

RVIS EVS: -0.2
RVIS percentile EVS: 39.11

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.982

Gene Damage Prediction

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