SLC12A5-AS1

SLC12A5 and MMP9 antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 20:46013500-46022073

Links

ENSG00000204044 ∙ ∙ ∙ HGNC:53143 ∙ ∙ ∙ 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 SLC12A5-AS1 gene.

• not provided (63 variants)
• Metaphyseal anadysplasia 2 (17 variants)
• Inborn genetic diseases (5 variants)
• not specified (4 variants)
• Developmental and epileptic encephalopathy, 34 (1 variants)
• Developmental and epileptic encephalopathy, 34;Epilepsy, idiopathic generalized, susceptibility to, 14 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC12A5-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			42	22	13	77
Total	0	0	42	22	13

Variants in SLC12A5-AS1

This is a list of pathogenic ClinVar variants found in the SLC12A5-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
20-46013515-C-T			Conflicting classifications of pathogenicity (Sep 25, 2024)
20-46013517-G-C			Likely benign (May 21, 2024)
20-46013520-T-C			Likely benign (Apr 27, 2022)
20-46013544-C-T			Uncertain significance (Apr 03, 2022)
20-46013647-G-C			Likely benign (Mar 07, 2024)
20-46013657-G-C			Uncertain significance (Nov 12, 2024)
20-46013681-C-A			Likely benign (Apr 04, 2023)
20-46013694-C-T		not specified	Uncertain significance (Mar 12, 2024)
20-46013717-C-A		Metaphyseal anadysplasia 2	Uncertain significance (Jan 13, 2018)
20-46013717-C-T			Likely benign (May 02, 2024)
20-46013719-A-G			Uncertain significance (Nov 05, 2024)
20-46013725-G-A		Metaphyseal anadysplasia 2	Uncertain significance (Dec 24, 2024)
20-46013727-C-T			Uncertain significance (Oct 24, 2022)
20-46013739-C-G			Uncertain significance (Sep 21, 2024)
20-46013740-G-T		not specified	Uncertain significance (Mar 18, 2024)
20-46013741-C-G			Likely benign (Dec 01, 2023)
20-46013756-C-G			Likely benign (Aug 10, 2023)
20-46013756-C-T			Likely benign (Jun 09, 2023)
20-46013757-T-G			Uncertain significance (Aug 31, 2024)
20-46013765-G-C			Uncertain significance (May 04, 2024)
20-46013766-C-A		MMP9-related disorder	Likely benign (Oct 30, 2024)
20-46013767-G-C		not specified • Metaphyseal anadysplasia 2	Benign (Feb 03, 2025)
20-46013767-G-T			Uncertain significance (Aug 14, 2024)
20-46013771-C-G			Likely benign (Oct 09, 2023)
20-46013773-C-G		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP