LCT-AS1

LCT antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 2:135820191-135829548

Links

ENSG00000226806 ∙ NCBI:100507600 ∙ ∙ HGNC:40337 ∙ ∙ ∙ 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 LCT-AS1 gene.

• not provided (9 variants)
• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCT-AS1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	3	1	9
Total	0	0	5	3	1

Variants in LCT-AS1

This is a list of pathogenic ClinVar variants found in the LCT-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-135821840-A-G			Benign (Jun 20, 2021)
2-135822000-A-C			Likely benign (Oct 17, 2022)
2-135822001-A-G			Likely benign (Nov 19, 2023)
2-135822003-AG-A			Likely benign (Nov 02, 2023)
2-135822008-A-G			Likely benign (Apr 13, 2021)
2-135822034-T-C			Likely benign (Nov 28, 2022)
2-135822040-A-G		LCT-related disorder	Likely benign (Jan 06, 2024)
2-135822058-A-C			Uncertain significance (Nov 27, 2023)
2-135822071-A-G		Inborn genetic diseases	Uncertain significance (May 27, 2022)
2-135822081-C-T		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
2-135822087-C-T		Inborn genetic diseases	Uncertain significance (Mar 12, 2022)
2-135822092-T-C		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
2-135822093-T-A			Uncertain significance (Oct 29, 2023)
2-135823784-T-G			Benign (Jun 19, 2021)
2-135823884-A-T			Likely benign (Jan 07, 2024)
2-135823920-C-G			Likely benign (Oct 13, 2023)
2-135823923-A-G			Likely benign (Mar 24, 2023)
2-135823932-G-A			Likely benign (Oct 07, 2022)
2-135823939-A-G			Uncertain significance (Mar 11, 2022)
2-135823947-G-A			Likely benign (Feb 03, 2022)
2-135823961-G-A			Uncertain significance (Aug 31, 2021)
2-135823968-G-A		Congenital lactase deficiency	Conflicting classifications of pathogenicity (Dec 18, 2023)
2-135823999-A-G			Uncertain significance (Aug 04, 2023)
2-135824004-C-A		LCT-related disorder	Likely pathogenic (Oct 11, 2022)
2-135824013-A-G			Likely benign (Jul 26, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP