SZT2-AS1

SZT2 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 1:43447776-43448644

Links

ENSG00000229372 ∙ ∙ ∙ HGNC:41225 ∙ ∙ ∙ 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 SZT2-AS1 gene.

• not provided (148 variants)
• Developmental and epileptic encephalopathy, 18 (42 variants)
• Inborn genetic diseases (40 variants)
• not specified (3 variants)
• Generalized epilepsy;Global developmental delay;Obesity (1 variants)
• SZT2-related condition (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SZT2-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)			3	1		4
splice region						0
non coding	7	1	100	52	1	161
Total	7	1	103	53	1

Highest pathogenic variant AF is 0.0000131

Variants in SZT2-AS1

This is a list of pathogenic ClinVar variants found in the SZT2-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
1-43447832-C-T			Likely benign (Dec 16, 2022)
1-43447837-C-T		not specified • Developmental and epileptic encephalopathy, 18	Benign (Feb 01, 2024)
1-43447838-G-A			Likely benign (Nov 22, 2022)
1-43447846-C-G			Uncertain significance (Oct 25, 2022)
1-43447858-C-T			Likely benign (Dec 09, 2023)
1-43447860-A-G		SZT2-related disorder • Developmental and epileptic encephalopathy, 18	Uncertain significance (May 10, 2023)
1-43447867-C-T			Likely benign (Mar 18, 2020)
1-43447868-T-C		Inborn genetic diseases • Developmental and epileptic encephalopathy, 18	Uncertain significance (Apr 11, 2023)
1-43447869-C-G			Uncertain significance (Oct 13, 2023)
1-43447880-C-G			Uncertain significance (Oct 29, 2021)
1-43447881-G-A		Inborn genetic diseases • Developmental and epileptic encephalopathy, 18	Uncertain significance (Aug 24, 2023)
1-43447886-C-T		SZT2-related disorder	Pathogenic (Mar 06, 2021)
1-43447888-G-C		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
1-43447889-G-A			Uncertain significance (Aug 04, 2021)
1-43447890-A-C			Uncertain significance (Jul 26, 2022)
1-43447894-C-T		Developmental and epileptic encephalopathy, 18	Likely benign (Dec 12, 2023)
1-43447895-T-C			Uncertain significance (Aug 20, 2019)
1-43447899-ATGTGTCTC-A			Pathogenic (Jul 01, 2022)
1-43447905-C-G			Uncertain significance (Sep 02, 2021)
1-43447909-G-A			Likely benign (Aug 01, 2022)
1-43447911-TTGTC-T			Pathogenic (Oct 16, 2023)
1-43447915-C-T			Likely benign (Feb 01, 2023)
1-43447922-T-C			Uncertain significance (Nov 27, 2023)
1-43447924-T-C			Likely benign (Jul 01, 2024)
1-43447923-G-GTGC			Uncertain significance (Apr 21, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP