LANCL2

LanC like glutathione S-transferase 2

Basic information

Region (hg38): 7:55365337-55433737

Previous symbols: [ "GPR69B" ]

Links

ENSG00000132434 ∙ NCBI:55915 ∙ OMIM:612919 ∙ HGNC:6509 ∙ Uniprot:Q9NS86 ∙ 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 LANCL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LANCL2 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			31	2		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	31	2	1

Variants in LANCL2

This is a list of pathogenic ClinVar variants found in the LANCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-55366032-G-A		not specified	Uncertain significance (May 31, 2023)
7-55366036-C-T		not specified	Uncertain significance (Jan 23, 2023)
7-55366111-C-T		not specified	Uncertain significance (Feb 03, 2022)
7-55366117-A-G		not specified	Uncertain significance (Oct 27, 2022)
7-55366128-G-C		not specified	Uncertain significance (Oct 12, 2021)
7-55366135-C-A		not specified	Uncertain significance (Dec 21, 2023)
7-55366137-C-G		not specified	Uncertain significance (Jun 07, 2024)
7-55366147-C-T		not specified	Uncertain significance (Mar 14, 2023)
7-55366156-C-T		not specified	Uncertain significance (Nov 30, 2021)
7-55366174-T-C		not specified	Likely benign (Oct 25, 2023)
7-55366188-A-C		not specified	Uncertain significance (Feb 28, 2024)
7-55366203-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-55366215-C-T		not specified	Uncertain significance (Aug 10, 2021)
7-55366217-T-G		not specified	Uncertain significance (Aug 30, 2021)
7-55398486-C-G		not specified	Uncertain significance (Dec 17, 2023)
7-55398491-G-T		not specified	Uncertain significance (Jul 20, 2022)
7-55398497-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-55398533-G-T		not specified	Uncertain significance (Jul 12, 2023)
7-55399974-G-T		not specified	Uncertain significance (Apr 06, 2024)
7-55399989-A-G		not specified	Likely benign (Oct 12, 2022)
7-55400081-G-A		not specified	Uncertain significance (Apr 07, 2022)
7-55401175-T-C		not specified	Uncertain significance (Jan 22, 2024)
7-55401277-G-C		not specified	Uncertain significance (Nov 27, 2023)
7-55411911-C-T		not specified	Uncertain significance (Oct 29, 2021)
7-55411920-T-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LANCL2	protein_coding	protein_coding	ENST00000254770	9	68295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.313	0.687	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.771	224	259	0.865	0.0000154	2850
Missense in Polyphen		101	131.21	0.76977		1332
Synonymous	-0.0684	105	104	1.01	0.00000644	886
Loss of Function	3.62	6	25.9	0.232	0.00000144	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Necessary for abscisic acid (ABA) binding on the cell membrane and activation of the ABA signaling pathway in granulocytes. {ECO:0000269|PubMed:19667068}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.320
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.116
• hipred: Y
• hipred_score: 0.570
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.608

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lancl2
• Phenotype: renal/urinary system phenotype; normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of abscisic acid-activated signaling pathway;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;cytosol;plasma membrane;cortical actin cytoskeleton
• Molecular function: catalytic activity;protein binding;ATP binding;GTP binding;phosphatidylinositol-5-phosphate binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-4-phosphate binding