SLC6A1-AS1

SLC6A1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 3:11006098-11019224

Links

ENSG00000232287 ∙ ∙ ∙ HGNC:40546 ∙ ∙ ∙ 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 SLC6A1-AS1 gene.

• Myoclonic-astatic epilepsy (150 variants)
• not provided (74 variants)
• Inborn genetic diseases (25 variants)
• SLC6A1-related condition (5 variants)
• Intellectual disability (1 variants)
• Myoclonic-atonic epilepsy (1 variants)
• Autosomal dominant epilepsy (1 variants)
• Global developmental delay;Seizure (1 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC6A1-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	20	26	73	68	22	209
Total	20	26	73	68	22

Highest pathogenic variant AF is 0.0000131

Variants in SLC6A1-AS1

This is a list of pathogenic ClinVar variants found in the SLC6A1-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
3-11015683-G-A			Benign (Dec 19, 2019)
3-11016775-A-G			Likely benign (Jul 27, 2018)
3-11016816-T-C			Benign (Jul 15, 2018)
3-11016891-C-G			Likely benign (Aug 12, 2018)
3-11016978-C-T			Benign (Jul 26, 2018)
3-11016994-G-C			Benign (Jul 15, 2018)
3-11017119-G-A		Epilepsy with myoclonic atonic seizures	Likely pathogenic (Jun 01, 2022)
3-11017195-C-T			Likely benign (Jun 01, 2024)
3-11017207-G-A		Inborn genetic diseases • SLC6A1-related disorder	Likely benign (Apr 01, 2022)
3-11017216-C-A		Epilepsy with myoclonic atonic seizures	Conflicting classifications of pathogenicity (Oct 26, 2023)
3-11017216-C-T		Epilepsy with myoclonic atonic seizures	Likely benign (Aug 16, 2022)
3-11017217-G-A		Inborn genetic diseases • SLC6A1-related disorder • Epilepsy with myoclonic atonic seizures	Benign/Likely benign (Jan 30, 2025)
3-11017220-C-A		Epilepsy with myoclonic atonic seizures	Likely benign (Oct 05, 2022)
3-11017223-C-T		Epilepsy with myoclonic atonic seizures	Likely benign (Aug 28, 2023)
3-11017224-G-A		Epilepsy with myoclonic atonic seizures • Inborn genetic diseases	Conflicting classifications of pathogenicity (Jun 18, 2024)
3-11017234-TG-T		Epilepsy with myoclonic atonic seizures	Pathogenic (Jul 12, 2019)
3-11017238-C-T		Epilepsy with myoclonic atonic seizures	Likely benign (May 31, 2023)
3-11017239-G-A		Inborn genetic diseases • Epilepsy with myoclonic atonic seizures	Uncertain significance (Apr 01, 2023)
3-11017241-C-T		Epilepsy with myoclonic atonic seizures	Benign (Dec 02, 2023)
3-11017242-G-A		Epilepsy with myoclonic atonic seizures • Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 30, 2023)
3-11017248-A-G		Epilepsy with myoclonic atonic seizures	Uncertain significance (Jul 26, 2022)
3-11017248-A-T		Epilepsy with myoclonic atonic seizures	Uncertain significance (Oct 30, 2020)
3-11017249-T-C		Epilepsy with myoclonic atonic seizures	Benign (Feb 04, 2022)
3-11017251-T-C		Epilepsy with myoclonic atonic seizures	Benign (Feb 04, 2021)
3-11017256-C-T		SLC6A1-related disorder • Inborn genetic diseases • Epilepsy with myoclonic atonic seizures	Likely benign (Dec 27, 2023)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP