LNCTSI

lncRNA TGF-beta/SMAD3 pathway interacting, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 21:36430289-36627435

Links

ENSG00000230479 ∙ ∙ ∙ HGNC:56660 ∙ ∙ ∙ 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 LNCTSI gene.

• not provided (78 variants)
• Autosomal recessive nonsyndromic hearing loss 29 (66 variants)
• not specified (22 variants)
• Inborn genetic diseases (9 variants)
• Hearing impairment (5 variants)
• Vein of Galen aneurysmal malformation (4 variants)
• CLDN14-related condition (2 variants)
• Sensorineural hearing impairment (1 variants)
• Alport syndrome (1 variants)
• Hearing loss, autosomal recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LNCTSI 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	4	6	78	37	10	135
Total	4	6	78	37	10

Highest pathogenic variant AF is 0.0000526

Variants in LNCTSI

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

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

Position	Type	Phenotype	Significance	ClinVar
21-36460620-A-G		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Jan 13, 2018)
21-36460754-A-G		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Jan 13, 2018)
21-36460761-A-AT			Likely benign (Aug 13, 2019)
21-36460869-C-T		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Jan 13, 2018)
21-36460910-C-T		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Jan 13, 2018)
21-36460925-C-T		Autosomal recessive nonsyndromic hearing loss 29	Benign/Likely benign (Jul 17, 2018)
21-36460928-C-T		Autosomal recessive nonsyndromic hearing loss 29	Conflicting classifications of pathogenicity (Jun 29, 2020)
21-36460966-C-G		not specified • Autosomal recessive nonsyndromic hearing loss 29 • CLDN14-related disorder	Conflicting classifications of pathogenicity (Nov 25, 2019)
21-36460981-C-T		Inborn genetic diseases	Uncertain significance (Feb 13, 2023)
21-36461002-C-T		Autosomal recessive nonsyndromic hearing loss 29	Pathogenic/Likely pathogenic (Feb 26, 2019)
21-36461006-G-A		not specified • Autosomal recessive nonsyndromic hearing loss 29	Conflicting classifications of pathogenicity (Jan 01, 2024)
21-36461009-C-T		not specified • Autosomal recessive nonsyndromic hearing loss 29	Benign (Jan 31, 2024)
21-36461015-C-T		Autosomal recessive nonsyndromic hearing loss 29	Conflicting classifications of pathogenicity (Feb 01, 2023)
21-36461022-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 08, 2024)
21-36461031-GC-G		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Jun 04, 2021)
21-36461033-C-T			Uncertain significance (-)
21-36461035-G-A			Uncertain significance (Jun 25, 2022)
21-36461035-G-C		Inborn genetic diseases	Uncertain significance (Jul 27, 2022)
21-36461043-T-C			Uncertain significance (Aug 10, 2023)
21-36461050-C-A		Inborn genetic diseases	Uncertain significance (Nov 22, 2023)
21-36461050-CAGCTGGT-C		Autosomal recessive nonsyndromic hearing loss 29	Uncertain significance (Mar 26, 2024)
21-36461063-G-A		not specified • Autosomal recessive nonsyndromic hearing loss 29	Benign (Jan 26, 2024)
21-36461070-G-A			Uncertain significance (Jul 05, 2022)
21-36461074-C-T			Uncertain significance (Jan 02, 2024)
21-36461075-G-A		not specified • Autosomal recessive nonsyndromic hearing loss 29 • CLDN14-related disorder	Conflicting classifications of pathogenicity (Dec 20, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP