MLEC

malectin

Basic information

Region (hg38): 12:120687148-120701859

Previous symbols: [ "KIAA0152" ]

Links

ENSG00000110917 ∙ NCBI:9761 ∙ OMIM:613802 ∙ HGNC:28973 ∙ Uniprot:Q14165 ∙ 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 MLEC gene.

• Inborn genetic diseases (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MLEC 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	4	0	2

Variants in MLEC

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

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

Position	Type	Phenotype	Significance	ClinVar
12-120687408-G-A		not specified	Uncertain significance (Mar 24, 2023)
12-120691123-C-T			Benign (Jul 13, 2018)
12-120694297-C-T			Benign (Jan 10, 2019)
12-120694851-G-A		not specified	Uncertain significance (Dec 27, 2023)
12-120696377-A-C		not specified	Uncertain significance (Apr 07, 2022)
12-120696441-C-T		not specified	Uncertain significance (Aug 14, 2023)
12-120696471-A-G		not specified	Uncertain significance (Mar 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MLEC	protein_coding	protein_coding	ENST00000228506	5	14996

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.607	0.391	125729	0	2	125731	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.16	75	149	0.502	0.00000827	1877
Missense in Polyphen		24	59.085	0.40619		659
Synonymous	0.321	57	60.2	0.947	0.00000339	599
Loss of Function	2.60	2	11.5	0.173	5.90e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Carbohydrate-binding protein with a strong ligand preference for Glc2-N-glycan. May play a role in the early steps of protein N-glycosylation (By similarity). {ECO:0000250}.
• Pathway: Neutrophil degranulation;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.673
• ghis: 0.606

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mlec
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;protein folding;neutrophil degranulation
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane;specific granule membrane
• Molecular function: enzyme binding;carbohydrate binding