LAPTM5

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

Basic information

Region (hg38): 1:30732469-30757774

Links

ENSG00000162511 ∙ NCBI:7805 ∙ OMIM:601476 ∙ HGNC:29612 ∙ Uniprot:Q13571 ∙ 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 LAPTM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAPTM5 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			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in LAPTM5

This is a list of pathogenic ClinVar variants found in the LAPTM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-30733863-C-A		not specified	Uncertain significance (Oct 04, 2022)
1-30733878-A-T		not specified	Uncertain significance (Jun 18, 2024)
1-30733882-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-30735210-G-A		not specified	Uncertain significance (Oct 27, 2022)
1-30735246-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-30735258-A-G		not specified	Uncertain significance (Mar 04, 2024)
1-30738992-C-G		not specified	Uncertain significance (Jan 17, 2023)
1-30739022-T-C		not specified	Uncertain significance (Jul 12, 2022)
1-30741647-A-G		not specified	Uncertain significance (May 04, 2022)
1-30741701-C-G		not specified	Uncertain significance (Dec 15, 2023)
1-30742465-G-A		not specified	Uncertain significance (Sep 13, 2023)
1-30742535-C-A		not specified	Uncertain significance (Dec 16, 2023)
1-30742546-T-C		not specified	Uncertain significance (Feb 17, 2024)
1-30757694-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-30757735-C-G		not specified	Uncertain significance (Apr 15, 2022)
1-30757735-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-30757736-G-A		not specified	Uncertain significance (Nov 01, 2022)
1-30757736-G-C		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAPTM5	protein_coding	protein_coding	ENST00000294507	8	25352

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.900	0.0994	117851	0	1	117852	0.00000424

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.491	134	151	0.888	0.00000879	1707
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000946	0.00000946
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a special functional role during embryogenesis and in adult hematopoietic cells. {ECO:0000269|PubMed:8661146}.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.144
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.41

Haploinsufficiency Scores

• pHI: 0.149
• hipred: Y
• hipred_score: 0.701
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Laptm5
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cellular response to leukemia inhibitory factor
• Cellular component: lysosome;lysosomal membrane;integral component of plasma membrane;membrane
• Molecular function: protein binding