LANCL3

LanC like family member 3

Basic information

Region (hg38): X:37571568-37684463

Links

ENSG00000147036 ∙ NCBI:347404 ∙ ∙ HGNC:24767 ∙ Uniprot:Q6ZV70 ∙ 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 LANCL3 gene.

• Inborn genetic diseases (18 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LANCL3 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				5	1	6
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	18	5	1

Variants in LANCL3

This is a list of pathogenic ClinVar variants found in the LANCL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-37571911-A-T		not specified	Uncertain significance (Mar 17, 2023)
X-37572001-C-A		not specified	Uncertain significance (Dec 01, 2022)
X-37572039-G-A		not specified	Uncertain significance (Jan 04, 2024)
X-37572042-G-C		not specified	Uncertain significance (May 09, 2022)
X-37572057-G-T		not specified	Uncertain significance (Oct 04, 2022)
X-37572138-G-C		not specified	Uncertain significance (May 25, 2022)
X-37572204-C-G		not specified	Uncertain significance (Jun 14, 2023)
X-37572212-C-T			Likely benign (Dec 01, 2022)
X-37572217-C-T		not specified	Uncertain significance (Oct 27, 2022)
X-37572243-G-T		not specified	Uncertain significance (Dec 14, 2023)
X-37572270-G-A		not specified	Uncertain significance (May 17, 2023)
X-37572300-G-T		not specified	Uncertain significance (Sep 22, 2023)
X-37572324-G-A		not specified	Uncertain significance (Jun 09, 2022)
X-37572360-G-C		not specified	Uncertain significance (Jul 08, 2022)
X-37572374-C-T			Likely benign (May 01, 2022)
X-37655754-A-G		not specified	Uncertain significance (Apr 22, 2022)
X-37655794-A-G		not specified	Uncertain significance (Jan 23, 2023)
X-37659458-A-G			Likely benign (Mar 01, 2023)
X-37659605-G-A		not specified	Uncertain significance (Nov 22, 2021)
X-37659631-G-A			Benign (Jan 12, 2018)
X-37659652-C-T			Likely benign (Nov 01, 2022)
X-37667321-A-T		not specified	Uncertain significance (Oct 04, 2022)
X-37667328-G-A			Likely benign (Apr 01, 2023)
X-37667330-A-G		not specified	Uncertain significance (Apr 04, 2023)
X-37667461-A-G		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LANCL3	protein_coding	protein_coding	ENST00000378619	5	112895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0427	0.932	125671	2	5	125678	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.142	143	148	0.967	0.0000109	2633
Missense in Polyphen		48	49.88	0.9623		920
Synonymous	-1.67	86	68.5	1.26	0.00000535	876
Loss of Function	1.94	4	10.9	0.366	7.49e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000404	0.000298
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000569	0.0000327
Other	0.000262	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0945

Haploinsufficiency Scores

• pHI: 0.0620
• hipred: N
• hipred_score: 0.441
• ghis: 0.380

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.232

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lancl3
• Phenotype: normal phenotype

Gene ontology

• Cellular component: plasma membrane
• Molecular function: catalytic activity