LAMP5

lysosomal associated membrane protein family member 5, the group of Lysosome associated membrane proteins

Basic information

Region (hg38): 20:9514358-9530524

Previous symbols: [ "C20orf103" ]

Links

ENSG00000125869 ∙ NCBI:24141 ∙ OMIM:614641 ∙ HGNC:16097 ∙ Uniprot:Q9UJQ1 ∙ 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 LAMP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMP5 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			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in LAMP5

This is a list of pathogenic ClinVar variants found in the LAMP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-9514880-A-G		not specified	Likely benign (Nov 19, 2022)
20-9515470-A-G		not specified	Uncertain significance (Nov 28, 2023)
20-9515522-A-T		not specified	Uncertain significance (Sep 28, 2022)
20-9515602-G-A		not specified	Uncertain significance (Jun 22, 2023)
20-9516083-A-C		not specified	Uncertain significance (Aug 08, 2023)
20-9516111-C-T		not specified	Uncertain significance (Apr 12, 2022)
20-9516317-T-C		not specified	Uncertain significance (Jun 12, 2023)
20-9518043-G-C		not specified	Uncertain significance (Sep 14, 2023)
20-9518097-A-T		not specified	Uncertain significance (Jul 20, 2021)
20-9518157-C-T		not specified	Likely benign (Aug 13, 2021)
20-9518192-C-A		not specified	Uncertain significance (Jun 30, 2022)
20-9518216-G-T		not specified	Uncertain significance (Aug 17, 2022)
20-9529651-G-A		not specified	Uncertain significance (Jul 05, 2022)
20-9529688-G-C		not specified	Uncertain significance (Mar 31, 2022)
20-9529690-C-T		not specified	Uncertain significance (Jan 10, 2022)
20-9529728-G-A		not specified	Uncertain significance (Apr 12, 2024)
20-9529749-G-A		not specified	Likely benign (Apr 15, 2024)
20-9529781-G-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMP5	protein_coding	protein_coding	ENST00000246070	6	16167

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.65e-9	0.0845	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.200	165	158	1.04	0.00000786	1845
Missense in Polyphen		63	61.494	1.0245		774
Synonymous	-0.202	65	63.0	1.03	0.00000344	536
Loss of Function	-0.0855	13	12.7	1.03	5.48e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000159
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in short-term synaptic plasticity in a subset of GABAergic neurons in the brain. {ECO:0000250|UniProtKB:Q9D387}.

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.423
• hipred: N
• hipred_score: 0.361
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lamp5

Gene ontology

• Cellular component: lysosome;late endosome;plasma membrane;endosome membrane;integral component of membrane;cell junction;cytoplasmic vesicle membrane;synaptic vesicle membrane;early endosome membrane;growth cone membrane;dendrite membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;recycling endosome membrane