LCTL

lactase like, the group of Glycoside hydrolase family 1

Basic information

Region (hg38): 15:66547179-66565998

Links

ENSG00000188501 ∙ NCBI:197021 ∙ OMIM:617060 ∙ HGNC:15583 ∙ Uniprot:Q6UWM7 ∙ 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 LCTL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCTL 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				2	1	3
missense			59	6		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	59	8	2

Variants in LCTL

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

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

Position	Type	Phenotype	Significance	ClinVar
15-66548575-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-66548576-T-C		not specified	Uncertain significance (Feb 23, 2023)
15-66548586-C-T		not specified	Uncertain significance (Apr 25, 2022)
15-66551672-T-C		not specified	Uncertain significance (Feb 18, 2025)
15-66551676-G-C		not specified	Uncertain significance (Feb 09, 2023)
15-66551681-C-G		not specified	Uncertain significance (Oct 20, 2021)
15-66551727-G-A		not specified	Uncertain significance (Dec 26, 2023)
15-66551733-G-A		not specified	Uncertain significance (Dec 17, 2023)
15-66551745-T-C		not specified	Uncertain significance (Jan 24, 2025)
15-66551760-C-T		not specified	Uncertain significance (Jan 24, 2023)
15-66551802-C-G		not specified	Uncertain significance (Jan 04, 2024)
15-66551810-T-C		not specified	Uncertain significance (Aug 03, 2022)
15-66551847-C-T		not specified	Uncertain significance (Jan 29, 2025)
15-66551859-T-G		not specified	Uncertain significance (Oct 19, 2024)
15-66552051-A-G		not specified	Uncertain significance (Mar 29, 2023)
15-66552126-G-T		not specified	Uncertain significance (Jul 25, 2023)
15-66552130-C-T		not specified	Uncertain significance (Jan 10, 2025)
15-66552138-A-G		not specified	Likely benign (Dec 01, 2022)
15-66552998-G-A		not specified	Uncertain significance (Dec 29, 2024)
15-66553039-G-C		not specified	Uncertain significance (Dec 10, 2024)
15-66553060-G-T		not specified	Uncertain significance (Jun 23, 2023)
15-66553085-G-A		not specified	Uncertain significance (Feb 06, 2024)
15-66553085-G-T		not specified	Uncertain significance (Jan 16, 2024)
15-66553111-C-T		not specified	Uncertain significance (Sep 01, 2021)
15-66553132-G-A		not specified	Likely benign (Apr 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCTL	protein_coding	protein_coding	ENST00000341509	13	18801

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.60e-20	0.00822	125636	0	111	125747	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.881	283	328	0.863	0.0000184	3716
Missense in Polyphen		122	139.53	0.87437		1564
Synonymous	-0.258	135	131	1.03	0.00000832	1043
Loss of Function	0.476	31	34.0	0.912	0.00000162	382

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000511	0.000510
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00125	0.00125
Finnish	0.000147	0.000139
European (Non-Finnish)	0.000213	0.000211
Middle Eastern	0.00125	0.00125
South Asian	0.00131	0.00127
Other	0.00104	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.919
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.68

Haploinsufficiency Scores

• pHI: 0.0748
• hipred: N
• hipred_score: 0.197
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.269

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lctl
• Phenotype: normal phenotype

Gene ontology

• Biological process: carbohydrate metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;brush border;integral component of membrane
• Molecular function: beta-glucosidase activity