LAPTM4B

lysosomal protein transmembrane 4 beta

Basic information

Region (hg38): 8:97775057-97853013

Links

ENSG00000104341 ∙ NCBI:55353 ∙ OMIM:613296 ∙ HGNC:13646 ∙ Uniprot:Q86VI4 ∙ 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 LAPTM4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAPTM4B 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					2	2
missense			16	2		18
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	16	2	3

Variants in LAPTM4B

This is a list of pathogenic ClinVar variants found in the LAPTM4B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-97775784-C-T			Benign (Jan 19, 2018)
8-97775803-G-C		not specified	Likely benign (Jun 03, 2024)
8-97775833-C-T		not specified	Uncertain significance (Oct 13, 2023)
8-97775858-G-A		not specified	Uncertain significance (Jan 25, 2023)
8-97775872-G-A		not specified	Uncertain significance (Aug 12, 2021)
8-97775926-C-G		not specified	Uncertain significance (Jan 31, 2024)
8-97775935-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-97775936-G-C		not specified	Uncertain significance (Nov 10, 2022)
8-97775937-C-CGGCGGGCTCCAGGCGA		not specified	Benign (Mar 29, 2016)
8-97775979-C-G		not specified	Likely benign (Aug 02, 2021)
8-97776032-C-G		not specified	Uncertain significance (May 15, 2023)
8-97776047-A-G		not specified	Uncertain significance (Oct 04, 2022)
8-97776094-G-C		not specified	Uncertain significance (Dec 20, 2022)
8-97805403-G-A			Benign (Feb 02, 2018)
8-97816062-G-A		not specified	Likely benign (Mar 07, 2023)
8-97816072-G-T		not specified	Uncertain significance (May 05, 2023)
8-97816076-A-G		not specified	Uncertain significance (Jun 06, 2023)
8-97816173-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-97819170-A-G		not specified	Uncertain significance (Aug 05, 2023)
8-97825061-T-C		not specified	Uncertain significance (Jan 26, 2022)
8-97825139-A-G		not specified	Uncertain significance (Apr 25, 2023)
8-97825146-A-G		not specified	Uncertain significance (Aug 02, 2021)
8-97825152-C-T		not specified	Uncertain significance (Sep 27, 2021)
8-97851418-G-A		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAPTM4B	protein_coding	protein_coding	ENST00000445593	7	77957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.28e-13	0.00701	125527	0	218	125745	0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.113	176	172	1.02	0.00000877	1984
Missense in Polyphen		56	62.588	0.89473		770
Synonymous	-0.729	78	70.2	1.11	0.00000384	643
Loss of Function	-0.849	17	13.6	1.25	6.64e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00175	0.00175
Ashkenazi Jewish	0.000699	0.000695
East Asian	0.00	0.00
Finnish	0.000788	0.000739
European (Non-Finnish)	0.000975	0.000959
Middle Eastern	0.00	0.00
South Asian	0.000610	0.000523
Other	0.00312	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for optimal lysosomal function (PubMed:21224396). Blocks EGF-stimulated EGFR intraluminal sorting and degradation. Conversely by binding with the phosphatidylinositol 4,5-bisphosphate, regulates its PIP5K1C interaction, inhibits HGS ubiquitination and relieves LAPTM4B inhibition of EGFR degradation (PubMed:25588945). Recruits SLC3A2 and SLC7A5 (the Leu transporter) to the lysosome, promoting entry of leucine and other essential amino acid (EAA) into the lysosome, stimulating activation of proton-transporting vacuolar (V)-ATPase protein pump (V-ATPase) and hence mTORC1 activation (PubMed:25998567). Plays a role as negative regulator of TGFB1 production in regulatory T cells (PubMed:26126825). Binds ceramide and facilitates its exit from late endosome in order to control cell death pathways (PubMed:26280656). {ECO:0000269|PubMed:21224396, ECO:0000269|PubMed:25588945, ECO:0000269|PubMed:25998567, ECO:0000269|PubMed:26126825, ECO:0000269|PubMed:26280656}.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.718
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.488
• hipred: N
• hipred_score: 0.123
• ghis: 0.494

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0396

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Laptm4b
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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)

Gene ontology

• Biological process: endosome organization;endosome transport via multivesicular body sorting pathway;negative regulation of transforming growth factor beta1 production;regulation of lysosomal membrane permeability;negative regulation of lysosomal protein catabolic process;regulation of lysosome organization
• Cellular component: lysosome;lysosomal membrane;endosome;early endosome;plasma membrane;membrane;integral component of membrane;late endosome membrane;multivesicular body membrane;cell projection;multivesicular body, internal vesicle
• Molecular function: protein binding;kinase binding;ubiquitin protein ligase binding;ceramide binding;phosphatidylinositol bisphosphate binding