LAPTM4A

lysosomal protein transmembrane 4 alpha

Basic information

Region (hg38): 2:20032650-20051628

Previous symbols: [ "MBNT" ]

Links

ENSG00000068697 ∙ NCBI:9741 ∙ OMIM:618837 ∙ HGNC:6924 ∙ Uniprot:Q15012 ∙ 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 LAPTM4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAPTM4A 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in LAPTM4A

This is a list of pathogenic ClinVar variants found in the LAPTM4A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-20033218-T-G		not specified	Uncertain significance (May 23, 2023)
2-20033252-C-T		not specified	Uncertain significance (Aug 16, 2021)
2-20033257-A-G		not specified	Uncertain significance (Sep 15, 2021)
2-20034357-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-20037335-T-C		not specified	Uncertain significance (Feb 28, 2024)
2-20037401-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-20037591-C-T		not specified	Uncertain significance (Jul 27, 2021)
2-20040899-C-A		not specified	Uncertain significance (Oct 05, 2023)
2-20040918-T-C		not specified	Uncertain significance (May 14, 2024)
2-20051411-A-C		not specified	Uncertain significance (Apr 22, 2024)
2-20051483-C-T		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAPTM4A	protein_coding	protein_coding	ENST00000175091	7	19379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00424	0.965	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0490	131	129	1.01	0.00000636	1521
Missense in Polyphen		36	38.512	0.93476		509
Synonymous	0.253	46	48.2	0.954	0.00000264	440
Loss of Function	1.89	6	13.5	0.445	7.40e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000886	0.0000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.000462	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in the transport of nucleosides and/or nucleoside derivatives between the cytosol and the lumen of an intracellular membrane-bound compartment. {ECO:0000250}.
• Pathway: Lysosome - Homo sapiens (human);EGFR1 (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.435
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.433
• hipred: Y
• hipred_score: 0.595
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Laptm4a
• Phenotype: homeostasis/metabolism phenotype; 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); vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Cellular component: lysosomal membrane;Golgi apparatus;membrane;integral component of membrane;late endosome membrane
• Molecular function: protein binding