LUCAT1

lung cancer associated transcript 1, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 5:91054834-91314547

Links

ENSG00000248323 ∙ NCBI:100505994 ∙ OMIM:618190 ∙ HGNC:48498 ∙ ∙ ∙ 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 LUCAT1 gene.

• not provided (201 variants)
• Usher syndrome type 2C (32 variants)
• not specified (25 variants)
• Inborn genetic diseases (6 variants)
• Febrile seizures, familial, 4;Usher syndrome type 2C (2 variants)
• Usher syndrome type 2C;Febrile seizures, familial, 4 (2 variants)
• Febrile seizures, familial, 4 (1 variants)
• Usher syndrome (1 variants)
• ADGRV1-related condition (1 variants)
• Retinal dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LUCAT1 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	8	3	95	88	22	216
Total	8	3	95	88	22

Highest pathogenic variant AF is 0.0000329

Variants in LUCAT1

This is a list of pathogenic ClinVar variants found in the LUCAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-91072321-C-G			Likely benign (Feb 21, 2019)
5-91072427-T-C			Likely benign (May 18, 2023)
5-91072427-T-G			Likely benign (Oct 28, 2023)
5-91072434-A-T		Usher syndrome type 2C	Conflicting classifications of pathogenicity (Jan 29, 2024)
5-91072448-T-G			Uncertain significance (May 28, 2020)
5-91072462-C-T			Likely benign (Jan 31, 2024)
5-91072463-G-A			Likely benign (Sep 27, 2023)
5-91072472-G-A			Likely benign (Jan 21, 2024)
5-91072474-T-C			Likely benign (Sep 10, 2021)
5-91072475-T-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 29, 2023)
5-91072476-T-C			Uncertain significance (May 17, 2022)
5-91072478-T-C			Uncertain significance (Nov 01, 2022)
5-91072489-T-C		not specified	Likely benign (Nov 02, 2023)
5-91072503-C-T			Conflicting classifications of pathogenicity (Jan 26, 2024)
5-91072504-G-A			Likely benign (Aug 29, 2023)
5-91072504-G-T			Likely benign (Apr 12, 2023)
5-91072505-T-A		not specified	Uncertain significance (Oct 06, 2016)
5-91072508-C-T			Conflicting classifications of pathogenicity (Oct 23, 2023)
5-91072510-C-T			Likely benign (Sep 17, 2023)
5-91072511-G-A		Retinal dystrophy • Usher syndrome type 2C	Conflicting classifications of pathogenicity (Dec 11, 2023)
5-91072522-C-T		Usher syndrome type 2C	Conflicting classifications of pathogenicity (Jan 16, 2024)
5-91072523-G-A			Conflicting classifications of pathogenicity (Sep 21, 2023)
5-91072528-G-A			Likely benign (Oct 22, 2023)
5-91072537-T-C			Likely benign (Sep 15, 2021)
5-91072544-C-T			Pathogenic (Aug 12, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP