SYNGAP1-AS1

SYNGAP1 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 6:33436829-33454470

Links

ENSG00000274259 ∙ ∙ ∙ HGNC:53831 ∙ ∙ ∙ 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 SYNGAP1-AS1 gene.

• Intellectual disability, autosomal dominant 5 (798 variants)
• not provided (294 variants)
• Inborn genetic diseases (131 variants)
• not specified (42 variants)
• Complex neurodevelopmental disorder (13 variants)
• Intellectual disability (10 variants)
• SYNGAP1-related condition (10 variants)
• See cases (6 variants)
• SYNGAP1-related developmental and epileptic encephalopathy (4 variants)
• Global developmental delay (2 variants)
• Seizure (2 variants)
• Microcephaly;Epileptic encephalopathy (1 variants)
• 13 conditions (1 variants)
• Developmental disorder (1 variants)
• SYNGAP1-related encephalopathy (1 variants)
• Neurodevelopmental disorder (1 variants)
• Neurodevelopmental delay (1 variants)
• Absent speech;Cerebellar ataxia;Global developmental delay (1 variants)
• SYNGAP1-Related Disorder (1 variants)
• Intellectual disability, autosomal dominant 5;Infantile epileptic dyskinetic encephalopathy (1 variants)
• Autosomal dominant epilepsy (1 variants)
• Marfanoid habitus and intellectual disability (1 variants)
• Motor delay;Atypical behavior;Global developmental delay;Delayed speech and language development (1 variants)
• Generalized hypotonia;Stereotypic movement disorder;Delayed speech and language development;Preauricular skin tag;Global developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYNGAP1-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)			1	1		2
splice region						0
non coding	175	84	338	373	69	1039
Total	175	84	339	374	69

Variants in SYNGAP1-AS1

This is a list of pathogenic ClinVar variants found in the SYNGAP1-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
6-33437403-G-A			Benign (Jul 17, 2018)
6-33437546-C-T			Likely benign (Jul 03, 2018)
6-33437660-C-T		Intellectual disability, autosomal dominant 5	Likely benign (Jun 11, 2023)
6-33437661-A-T		Intellectual disability, autosomal dominant 5	Likely benign (Jan 03, 2024)
6-33437663-G-A		Intellectual disability, autosomal dominant 5	Likely benign (Aug 14, 2021)
6-33437663-G-C		Intellectual disability, autosomal dominant 5	Likely benign (Nov 10, 2022)
6-33437667-G-A			Pathogenic (Nov 25, 2022)
6-33437670-C-T		Intellectual disability, autosomal dominant 5	Likely benign (Jun 14, 2022)
6-33437672-A-G		Intellectual disability, autosomal dominant 5	Likely pathogenic (Nov 04, 2022)
6-33437678-G-A		Intellectual disability, autosomal dominant 5	Benign/Likely benign (Oct 13, 2023)
6-33437680-C-T		Intellectual disability, autosomal dominant 5	Uncertain significance (Jul 06, 2022)
6-33437684-TAGAC-T		Intellectual disability, autosomal dominant 5	Pathogenic (Jul 02, 2018)
6-33437685-A-T		Intellectual disability, autosomal dominant 5	Likely benign (Feb 05, 2022)
6-33437691-T-C		Intellectual disability, autosomal dominant 5	Likely benign (Nov 24, 2023)
6-33437692-GTGCTAAAGC-G			Pathogenic (Oct 26, 2016)
6-33437695-C-T		Intellectual disability, autosomal dominant 5	Likely benign (Nov 19, 2021)
6-33437696-T-A		Intellectual disability, autosomal dominant 5	Uncertain significance (Mar 11, 2020)
6-33437709-C-T		Intellectual disability, autosomal dominant 5	Likely benign (Dec 14, 2023)
6-33437717-C-A		Intellectual disability, autosomal dominant 5	Pathogenic (Oct 31, 2022)
6-33437720-G-A		Intellectual disability, autosomal dominant 5	Uncertain significance (May 04, 2022)
6-33437721-G-A		Intellectual disability, autosomal dominant 5	Likely benign (Dec 13, 2023)
6-33437724-G-A		Intellectual disability, autosomal dominant 5	Likely benign (Apr 20, 2022)
6-33437724-G-T		Intellectual disability, autosomal dominant 5	Benign (Oct 13, 2023)
6-33437725-C-T			Likely benign (Jul 01, 2019)
6-33437726-T-A		Global developmental delay	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP