LEPROTL1

leptin receptor overlapping transcript like 1

Basic information

Region (hg38): 8:30095407-30177208

Links

ENSG00000104660 ∙ NCBI:23484 ∙ OMIM:607338 ∙ HGNC:6555 ∙ Uniprot:O95214 ∙ 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 LEPROTL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LEPROTL1 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			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in LEPROTL1

This is a list of pathogenic ClinVar variants found in the LEPROTL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-30101903-A-G		not specified	Uncertain significance (Jan 04, 2022)
8-30104300-C-A		not specified	Uncertain significance (Apr 01, 2024)
8-30104400-G-A		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
8-30104437-T-C		not specified	Uncertain significance (Jun 16, 2023)
8-30131945-A-G			Benign (Jul 29, 2018)
8-30131968-G-A		not specified	Likely benign (Dec 14, 2021)
8-30132091-T-C		not specified	Uncertain significance (Mar 20, 2023)
8-30132101-C-T		not specified	Uncertain significance (May 30, 2024)
8-30132128-T-C		not specified	Uncertain significance (Sep 28, 2021)
8-30132133-G-A		not specified	Uncertain significance (May 05, 2022)
8-30132214-A-G		not specified	Uncertain significance (Jun 07, 2024)
8-30132393-G-A			Benign (Feb 08, 2018)
8-30132423-A-T			Likely benign (Apr 26, 2018)
8-30132580-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-30132594-G-A			Likely benign (Sep 01, 2022)
8-30132640-G-A		not specified	Uncertain significance (Aug 10, 2021)
8-30132685-C-T			Benign (Jun 19, 2018)
8-30132718-C-G		not specified	Uncertain significance (Dec 27, 2023)
8-30132760-G-A		not specified	Uncertain significance (Aug 04, 2023)
8-30132787-A-G		not specified	Uncertain significance (Feb 28, 2023)
8-30137279-G-A		not specified	Uncertain significance (Sep 01, 2021)
8-30137289-C-A		not specified	Uncertain significance (Oct 18, 2021)
8-30138598-C-A		not specified	Uncertain significance (Jul 25, 2023)
8-30138628-T-C		not specified	Uncertain significance (May 14, 2024)
8-30138668-C-T		not specified	Likely benign (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LEPROTL1	protein_coding	protein_coding	ENST00000523116	4	81811

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.721	0.267	116475	0	1	116476	0.00000429

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.942	65	90.2	0.721	0.00000444	1069
Missense in Polyphen		13	29.644	0.43854		358
Synonymous	0.424	32	35.2	0.909	0.00000196	363
Loss of Function	1.90	0	4.21	0.00	1.75e-7	65

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)	0.00000923	0.00000923
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates growth hormone (GH) receptor cell surface expression in liver. May play a role in liver resistance to GH during periods of reduced nutrient availability. {ECO:0000269|PubMed:19907080}.

Recessive Scores

• pRec: 0.0924

Intolerance Scores

• loftool: 0.454
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.04

Haploinsufficiency Scores

• pHI: 0.262
• hipred: N
• hipred_score: 0.305
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.571

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Leprotl1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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

• Biological process: late endosome to vacuole transport via multivesicular body sorting pathway;negative regulation of protein localization to cell surface
• Cellular component: endosome;integral component of membrane
• Molecular function: protein binding