LANCL1

LanC like glutathione S-transferase 1

Basic information

Region (hg38): 2:210427131-210477652

Previous symbols: [ "GPR69A" ]

Links

ENSG00000115365 ∙ NCBI:10314 ∙ OMIM:604155 ∙ HGNC:6508 ∙ Uniprot:O43813 ∙ 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 LANCL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LANCL1 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
missense			32		1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	2

Variants in LANCL1

This is a list of pathogenic ClinVar variants found in the LANCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-210435393-A-G		not specified	Uncertain significance (Jul 15, 2021)
2-210436259-T-C		not specified	Uncertain significance (May 20, 2024)
2-210436274-G-C		not specified	Uncertain significance (Aug 10, 2023)
2-210436296-C-T		not specified	Uncertain significance (May 20, 2024)
2-210436298-T-G		not specified	Uncertain significance (Nov 29, 2021)
2-210436331-T-C		not specified	Uncertain significance (Feb 16, 2023)
2-210436335-G-T		not specified	Uncertain significance (Mar 24, 2023)
2-210436358-T-C		not specified	Uncertain significance (Oct 03, 2022)
2-210437692-T-C		not specified	Uncertain significance (Jun 29, 2023)
2-210437710-T-C		not specified	Uncertain significance (May 23, 2023)
2-210437728-C-T		not specified	Uncertain significance (Jul 20, 2021)
2-210440624-C-T		not specified	Uncertain significance (Apr 01, 2024)
2-210440633-G-A		not specified	Uncertain significance (Sep 12, 2023)
2-210441354-T-C		not specified	Uncertain significance (May 24, 2023)
2-210441359-A-C		not specified	Uncertain significance (Mar 07, 2024)
2-210441387-C-T		not specified	Uncertain significance (Dec 03, 2021)
2-210441399-A-G		not specified	Uncertain significance (Jun 16, 2023)
2-210441411-G-T		not specified	Uncertain significance (Mar 02, 2023)
2-210441437-A-C			Benign (Oct 24, 2018)
2-210455117-A-G		not specified	Uncertain significance (Oct 12, 2021)
2-210455162-C-T		not specified	Uncertain significance (Jun 09, 2022)
2-210455228-G-C		not specified	Uncertain significance (Jun 05, 2024)
2-210455233-T-C		not specified	Uncertain significance (Aug 12, 2021)
2-210455249-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-210455267-C-T		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LANCL1	protein_coding	protein_coding	ENST00000443314	9	46404

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.08e-11	0.163	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.743	248	217	1.14	0.0000108	2595
Missense in Polyphen		94	89.605	1.0491		1131
Synonymous	-0.278	85	81.8	1.04	0.00000400	755
Loss of Function	0.714	19	22.7	0.838	0.00000111	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000740	0.000726
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000326	0.000326
Finnish	0.000323	0.000323
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000326	0.000326
South Asian	0.00150	0.00134
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in EPS8 signaling. Binds glutathione. {ECO:0000269|PubMed:19528316}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.846
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

• pHI: 0.238
• hipred: N
• hipred_score: 0.350
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lancl1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway
• Cellular component: cytoplasm;plasma membrane;integral component of plasma membrane
• Molecular function: catalytic activity;G protein-coupled receptor activity;protein binding;zinc ion binding;SH3 domain binding;glutathione binding;low-density lipoprotein particle receptor binding