SPNS2-AS1

SPNS2 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 17:4487679-4499913

Links

ENSG00000229782 ∙ NCBI:107985053 ∙ ∙ HGNC:55787 ∙ ∙ ∙ 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 SPNS2-AS1 gene.

• not provided (5 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 SPNS2-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			4	1	3	8
Total	0	0	4	1	3

Variants in SPNS2-AS1

This is a list of pathogenic ClinVar variants found in the SPNS2-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
17-4487853-G-A		not specified	Uncertain significance (Jan 08, 2024)
17-4487868-G-A		not specified	Likely benign (Aug 20, 2024)
17-4487886-G-A		not specified	Uncertain significance (Feb 11, 2022)
17-4498679-G-A			Benign (May 16, 2021)
17-4498895-G-C			Benign (May 15, 2021)
17-4499083-C-G		SPNS2-related disorder	Likely benign (Sep 20, 2024)
17-4499098-G-T		not specified	Uncertain significance (Oct 01, 2024)
17-4499163-G-C		not specified	Uncertain significance (Dec 22, 2023)
17-4499168-G-T		not specified	Uncertain significance (May 30, 2024)
17-4499242-G-T		not specified	Uncertain significance (Aug 17, 2022)
17-4499252-A-C		not specified	Uncertain significance (Jul 08, 2021)
17-4499258-CCCCCCGGCA-C			Uncertain significance (-)
17-4499258-C-CCCCCCGGCA		SPNS2-related disorder	Uncertain significance (Jul 24, 2024)
17-4499260-C-T			Likely benign (Nov 01, 2022)
17-4499262-C-G		not specified	Uncertain significance (Nov 29, 2023)
17-4499263-C-T		SPNS2-related disorder	Benign (Nov 25, 2019)
17-4499267-A-C		not specified	Uncertain significance (Jul 09, 2021)
17-4499276-A-C		not specified	Uncertain significance (Dec 06, 2021)
17-4499334-G-C		not specified	Uncertain significance (Apr 09, 2024)
17-4499343-G-A		not specified	Uncertain significance (Aug 07, 2024)
17-4499508-T-C			Benign (May 15, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP