LAPTM5

protein-coding

lysosomal protein transmembrane 5, the group of MicroRNA protein coding host genes

Gene summary

This gene encodes a transmembrane receptor that is associated with lysosomes. The encoded protein, also known as E3 protein, may play a role in hematopoiesis. [provided by RefSeq, Feb 2009]

MANE transcript

NM_006762.3

Inheritance

—

ClinVar variants

U:42

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr1:30,732,469-30,757,774

External References & Databases

Ensembl (ENSG00000162511)

Transcript & Mutation Effects

hg38 • Region Span ~25.3 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 LAPTM5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006762.3. 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						0
missense			41 clinvar			41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	42	0	0	42

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006762.3	RefSeq	NP_006753.1	8	MANE Select
ENST00000294507.4	Ensembl	ENSP00000294507.3	8	MANE Select
ENST00000875062.1	Ensembl	ENSP00000545121.1	6	Standard
ENST00000875062.2	Ensembl	ENSP00000545121.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Lysosome - Homo sapiens (human)

Biological Process

cellular response to leukemia inhibitory factor

Molecular Function

protein binding

Cellular Component

lysosome
lysosomal membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294507
Coding exons: 8
Length: 25352
Individuals with no LoFs: 117851
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 117852
p: 0.00000424

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.491	134	151	0.888	0.00000879	1707
Missense (PolyPhen)		47	51.509	0.91246		599
Synonymous	-0.239	66	63.6	1.04	0.00000394	494
Loss of Function	2.92	1	11.9	0.0844	5.00e-7	154

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000095	0.0000095	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May have a special functional role during embryogenesis and in adult hematopoietic cells. {ECO:0000269|PubMed:8661146}.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.144
RVIS EVS: 0.28
RVIS percentile EVS: 71.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.933

Gene Damage Prediction

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