LAMP3

lysosomal associated membrane protein 3, the group of CD molecules|Lysosome associated membrane proteins

Basic information

Region (hg38): 3:183122214-183163839

Links

ENSG00000078081 ∙ NCBI:27074 ∙ OMIM:605883 ∙ HGNC:14582 ∙ Uniprot:Q9UQV4 ∙ 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 LAMP3 gene.

• Inborn genetic diseases (21 variants)
• not provided (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMP3 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			17	5		22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	5	0

Variants in LAMP3

This is a list of pathogenic ClinVar variants found in the LAMP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183124141-C-A		not specified	Uncertain significance (Mar 04, 2024)
3-183124158-CCA-C			Uncertain significance (Dec 18, 2017)
3-183124164-T-C		not specified	Uncertain significance (Aug 15, 2023)
3-183135816-C-T		not specified	Uncertain significance (Jan 18, 2022)
3-183135834-C-T		not specified	Uncertain significance (Mar 02, 2023)
3-183135858-C-T		not specified	Likely benign (Jan 07, 2022)
3-183135884-G-A		not specified	Uncertain significance (Mar 21, 2023)
3-183140562-C-T		not specified	Uncertain significance (Aug 21, 2023)
3-183152401-C-T		See cases	Uncertain significance (-)
3-183152423-G-T		not specified	Uncertain significance (Jul 17, 2023)
3-183152433-C-T		not specified	Likely benign (Jul 20, 2021)
3-183152449-C-T		not specified	Uncertain significance (Dec 14, 2022)
3-183152454-G-T		not specified	Uncertain significance (Nov 15, 2021)
3-183152455-C-T		not specified	Uncertain significance (May 25, 2022)
3-183152460-G-A		not specified	Uncertain significance (Jul 12, 2022)
3-183152476-T-C		not specified	Uncertain significance (Nov 02, 2023)
3-183153694-T-G		not specified	Uncertain significance (Nov 04, 2023)
3-183153715-C-T		not specified	Uncertain significance (Apr 20, 2023)
3-183153795-G-C		not specified	Uncertain significance (Sep 06, 2022)
3-183153897-C-T		not specified	Likely benign (Aug 22, 2023)
3-183153954-T-C		not specified	Uncertain significance (Feb 03, 2022)
3-183153965-G-T		not specified	Uncertain significance (May 24, 2023)
3-183154047-A-C		not specified	Uncertain significance (Dec 14, 2023)
3-183154050-G-A		not specified	Uncertain significance (Mar 01, 2023)
3-183154124-G-A		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMP3	protein_coding	protein_coding	ENST00000265598	6	41627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000267	0.938	125667	0	79	125746	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.284	221	233	0.948	0.0000125	2657
Missense in Polyphen		42	50.501	0.83166		614
Synonymous	0.851	83	93.5	0.888	0.00000571	887
Loss of Function	1.68	8	15.0	0.533	7.24e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000414
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00291	0.00291
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in dendritic cell function and in adaptive immunity. {ECO:0000269|PubMed:9768752}.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.301

Intolerance Scores

• loftool: 0.728
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.316
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0457

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lamp3

Gene ontology

• Biological process: adaptive immune response;regulation of autophagy;positive regulation of gene expression;response to interferon-alpha;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;viral entry into host cell;negative regulation of proteasomal protein catabolic process;regulation of viral life cycle
• Cellular component: lysosomal membrane;early endosome;plasma membrane;integral component of membrane;vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;alveolar lamellar body membrane