LECT2

leukocyte cell derived chemotaxin 2

Basic information

Region (hg38): 5:135922278-135954983

Links

ENSG00000145826 ∙ NCBI:3950 ∙ OMIM:602882 ∙ HGNC:6550 ∙ Uniprot:O14960 ∙ 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 LECT2 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LECT2 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in LECT2

This is a list of pathogenic ClinVar variants found in the LECT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-135947338-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-135947355-C-T		LECT2-related disorder	Likely benign (Jun 21, 2019)
5-135951265-T-C		not specified	Uncertain significance (Dec 13, 2023)
5-135951340-T-C		LECT2-related disorder	Benign (Oct 17, 2019)
5-135952922-T-C		not specified	Uncertain significance (Dec 15, 2022)
5-135952944-T-C		not specified	Uncertain significance (Sep 26, 2023)
5-135952958-C-T		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LECT2	protein_coding	protein_coding	ENST00000274507	4	32756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00148	0.693	125680	1	65	125746	0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0857	83	85.2	0.974	0.00000443	972
Missense in Polyphen		36	31.745	1.134		365
Synonymous	0.540	27	30.8	0.876	0.00000167	297
Loss of Function	0.748	5	7.16	0.698	3.68e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00175	0.00175
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a neutrophil chemotactic activity. Also a positive regulator of chondrocyte proliferation (PubMed:9524238). Does not show metalloendopeptidase activity (PubMed:27334921). {ECO:0000269|PubMed:27334921, ECO:0000269|PubMed:9524238}.
• Pathway: C-MYB transcription factor network (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.286

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lect2
• Phenotype: immune system phenotype; liver/biliary system phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: skeletal system development;chemotaxis
• Cellular component: extracellular space;cytoplasm
• Molecular function: protein binding;identical protein binding;metal ion binding