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.

• not_specified (58 variants)
• not_provided (4 variants)
• Prostate_cancer (1 variants)

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. These statistics are base on transcript: NM_001136049.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			57	2		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	57	3	1

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