NALCN-AS1

NALCN antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 13:100708325-101081764

Links

ENSG00000233009 ∙ NCBI:100885778 ∙ ∙ HGNC:42743 ∙ ∙ ∙ 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 NALCN-AS1 gene.

• not provided (42 variants)
• Inborn genetic diseases (9 variants)
• Congenital contractures of the limbs and face, hypotonia, and developmental delay (4 variants)
• not specified (1 variants)
• Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 (1 variants)
• Hypotonia, infantile, with psychomotor retardation and characteristic facies 1;Congenital contractures of the limbs and face, hypotonia, and developmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NALCN-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)			2			2
splice region						0
non coding			31	14	4	49
Total	0	0	33	14	4

Variants in NALCN-AS1

This is a list of pathogenic ClinVar variants found in the NALCN-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
13-101055303-C-G		Congenital contractures of the limbs and face, hypotonia, and developmental delay	Uncertain significance (May 04, 2018)
13-101055309-G-A			Uncertain significance (May 08, 2023)
13-101055318-C-T			Uncertain significance (Mar 18, 2022)
13-101055324-C-T		Congenital contractures of the limbs and face, hypotonia, and developmental delay	Uncertain significance (Nov 25, 2019)
13-101055325-G-A			Likely benign (Sep 28, 2022)
13-101055328-G-C		Inborn genetic diseases	Uncertain significance (Jan 22, 2024)
13-101055347-C-T			Uncertain significance (May 14, 2022)
13-101055348-G-A		Inborn genetic diseases	Uncertain significance (Mar 30, 2023)
13-101055348-G-C		Congenital contractures of the limbs and face, hypotonia, and developmental delay	Uncertain significance (-)
13-101055356-C-T			Uncertain significance (Sep 01, 2020)
13-101055374-C-T		Hypotonia, infantile, with psychomotor retardation and characteristic facies 1;Congenital contractures of the limbs and face, hypotonia, and developmental delay • Inborn genetic diseases	Uncertain significance (Aug 07, 2023)
13-101055375-C-T		not specified	Uncertain significance (Jun 20, 2024)
13-101055385-C-T		NALCN-related disorder	Conflicting classifications of pathogenicity (Feb 01, 2024)
13-101055386-G-A		Inborn genetic diseases	Uncertain significance (Oct 14, 2020)
13-101055387-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 12, 2024)
13-101055399-G-T			Uncertain significance (Jan 12, 2024)
13-101055414-C-T			Conflicting classifications of pathogenicity (Aug 17, 2023)
13-101055418-A-G			Likely benign (Jul 11, 2018)
13-101055425-A-G		not specified	Uncertain significance (Dec 19, 2023)
13-101055429-T-C			Uncertain significance (Jun 13, 2023)
13-101055432-T-C			Uncertain significance (Feb 21, 2023)
13-101055432-T-G			Uncertain significance (Jun 30, 2022)
13-101055433-C-T			Likely benign (May 08, 2023)
13-101055434-C-T			Uncertain significance (Jan 27, 2020)
13-101055435-T-G			Likely benign (Jan 08, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP