GSEC

G-quadruplex forming sequence containing lncRNA, the group of Long non-coding RNAs with non-systematic symbols

Basic information

Region (hg38): 11:126340776-126355591

Previous symbols: [ "ST3GAL4-AS1" ]

Links

ENSG00000280832 ∙ NCBI:399972 ∙ ∙ HGNC:48645 ∙ ∙ ∙ 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 GSEC gene.

• not provided (16 variants)
• Al-Raqad syndrome (6 variants)
• not specified (3 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 GSEC 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		2	10	12	1	25
Total	0	2	10	12	1

Highest pathogenic variant AF is 0.0000197

Variants in GSEC

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

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

Position	Type	Phenotype	Significance	ClinVar
11-126343301-A-G			Likely benign (Apr 01, 2021)
11-126343340-C-T			Uncertain significance (Dec 01, 2022)
11-126343344-G-A		Inborn genetic diseases	Uncertain significance (Aug 06, 2024)
11-126343347-G-A		Al-Raqad syndrome • DCPS-related disorder • Inborn genetic diseases	Benign/Likely benign (Jan 01, 2025)
11-126343361-C-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2023)
11-126343374-C-T		Al-Raqad syndrome • Inborn genetic diseases	Uncertain significance (Jul 08, 2021)
11-126343385-C-T		Inborn genetic diseases	Uncertain significance (Feb 26, 2024)
11-126343387-G-A		DCPS-related disorder	Benign (Jun 11, 2018)
11-126343394-A-G		not specified	Uncertain significance (Mar 04, 2025)
11-126343404-TCCACCAGGGGCAGGTGAGTGGCTTCACCAAA-T		not specified	Uncertain significance (Jun 06, 2024)
11-126343412-G-GGGCA			Uncertain significance (May 29, 2024)
11-126345351-C-T		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
11-126345365-T-C		Inborn genetic diseases	Uncertain significance (Jul 14, 2024)
11-126345368-C-T			Uncertain significance (Apr 11, 2017)
11-126345390-G-A			Conflicting classifications of pathogenicity (Dec 31, 2019)
11-126345390-G-T		Al-Raqad syndrome	Uncertain significance (Feb 07, 2018)
11-126345399-T-G		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
11-126345403-C-T		DCPS-related disorder	Benign/Likely benign (May 01, 2023)
11-126345443-G-A		Inborn genetic diseases	Uncertain significance (May 13, 2024)
11-126345454-C-T			Likely benign (Feb 01, 2025)
11-126345455-G-A		Inborn genetic diseases	Uncertain significance (Dec 15, 2023)
11-126345455-G-T		Al-Raqad syndrome	Likely pathogenic (Feb 24, 2023)
11-126345460-C-T			Likely benign (May 01, 2022)
11-126345464-G-A		not specified	Uncertain significance (Mar 01, 2022)
11-126345467-T-G		DCPS-related disorder	Likely benign (Mar 01, 2025)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP