LMLN

leishmanolysin like peptidase

Basic information

Region (hg38): 3:197960200-198043720

Links

ENSG00000185621 ∙ NCBI:89782 ∙ OMIM:609380 ∙ HGNC:15991 ∙ Uniprot:Q96KR4 ∙ 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 LMLN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMLN 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				1	1	2
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1		1	2
Total	0	0	22	1	2

Variants in LMLN

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

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

Position	Type	Phenotype	Significance	ClinVar
3-197960295-G-A		not specified	Uncertain significance (Jul 12, 2022)
3-197960309-C-G		not specified	Uncertain significance (Sep 15, 2021)
3-197960309-C-T		not specified	Uncertain significance (Sep 29, 2022)
3-197960319-G-C		not specified	Uncertain significance (Nov 19, 2022)
3-197960408-C-T		not specified	Uncertain significance (Feb 01, 2023)
3-197974368-T-A			Benign (Mar 29, 2018)
3-197974394-T-G		not specified	Uncertain significance (May 15, 2024)
3-197976084-G-A		not specified	Uncertain significance (Jul 08, 2022)
3-197976096-C-T		not specified	Uncertain significance (Jun 18, 2024)
3-197976118-C-G			Benign (Mar 27, 2018)
3-197976623-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-197976692-A-G		not specified	Likely benign (Jun 05, 2024)
3-197976705-A-G		not specified	Uncertain significance (Nov 07, 2023)
3-197983947-A-G		not specified	Uncertain significance (Mar 14, 2023)
3-197983957-A-T		not specified	Uncertain significance (Apr 12, 2022)
3-197990621-G-A		not specified	Uncertain significance (Oct 20, 2023)
3-197996195-T-C			Likely benign (Jun 26, 2018)
3-197996207-T-A			Benign (May 21, 2018)
3-197996244-G-T		Malignant tumor of prostate	Uncertain significance (-)
3-197996257-A-G		not specified	Uncertain significance (Nov 18, 2023)
3-197999311-C-G		not specified	Uncertain significance (Feb 23, 2023)
3-197999330-T-C		not specified	Uncertain significance (Dec 14, 2023)
3-198003073-T-G		not specified	Uncertain significance (Jan 23, 2024)
3-198024702-G-A		not specified	Uncertain significance (Jan 17, 2024)
3-198035876-C-G		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMLN	protein_coding	protein_coding	ENST00000420910	17	83521

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-14	0.937	125619	1	128	125748	0.000513

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	282	387	0.729	0.0000200	4503
Missense in Polyphen		69	126.95	0.5435		1515
Synonymous	0.300	140	145	0.968	0.00000793	1319
Loss of Function	2.22	29	45.1	0.643	0.00000250	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00124
Ashkenazi Jewish	0.00435	0.00428
East Asian	0.000342	0.000326
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000283	0.000273
Middle Eastern	0.000342	0.000326
South Asian	0.000428	0.000392
Other	0.000667	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloprotease. {ECO:0000250|UniProtKB:Q9VH19}.

Recessive Scores

• pRec: 0.454

Intolerance Scores

• loftool: 0.894
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.527
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.513

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmln

Zebrafish Information Network

• Gene name: lmln
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: dispersed

Gene ontology

• Biological process: proteolysis;cell cycle;cell adhesion;cell division
• Cellular component: cytoplasm;lipid droplet;cytosol;focal adhesion;membrane
• Molecular function: metalloendopeptidase activity;peptidase activity;metal ion binding