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NM_052867.4(NALCN):c.5138G>A (p.Gly1713Asp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 19, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001837377.2

Allele description [Variation Report for NM_052867.4(NALCN):c.5138G>A (p.Gly1713Asp)]

NM_052867.4(NALCN):c.5138G>A (p.Gly1713Asp)

Genes:
NALCN-AS1:NALCN antisense RNA 1 [Gene - HGNC]
NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q32.3
Genomic location:
Preferred name:
NM_052867.4(NALCN):c.5138G>A (p.Gly1713Asp)
HGVS:
  • NC_000013.11:g.101055374C>T
  • NG_053176.1:g.366833G>A
  • NM_001350748.2:c.5225G>A
  • NM_001350749.2:c.5138G>A
  • NM_001350750.2:c.5051G>A
  • NM_001350751.2:c.5051G>A
  • NM_052867.4:c.5138G>AMANE SELECT
  • NP_001337677.1:p.Gly1742Asp
  • NP_001337678.1:p.Gly1713Asp
  • NP_001337679.1:p.Gly1684Asp
  • NP_001337680.1:p.Gly1684Asp
  • NP_443099.1:p.Gly1713Asp
  • NC_000013.10:g.101707726C>T
  • NM_052867.2:c.5138G>A
  • NR_047687.1:n.698C>T
Protein change:
G1684D
Links:
dbSNP: rs2031085413
NCBI 1000 Genomes Browser:
rs2031085413
Molecular consequence:
  • NM_001350748.2:c.5225G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350749.2:c.5138G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350750.2:c.5051G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350751.2:c.5051G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_052867.4:c.5138G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_047687.1:n.698C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1 (INNFD)
Identifiers:
MONDO: MONDO:0024567; MedGen: C3809454; Orphanet: 371364; OMIM: 615419
Name:
Congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD)
Identifiers:
MONDO: MONDO:0014556; MedGen: C4225398; OMIM: 616266

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002097945New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Feb 19, 2021) 		inheritedclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center - CSER-NYCKidSeq, SCV002097945.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited heterozygous c.5138G>A (p.Gly1713Asp) missense variant identified in the NALCN gene has not been reported in affected individual in the literature. The variant has been reported once in the gnomAD(v3) database (1out of 152222 heterozygous alleles) suggesting it is not a common benign allele in the populations represented in that database.The variant affects an evolutionarily conserved residue and is predicted deleterious by multiple in silico tools. Functional studies to evaluate the potential consequencesof this variant have not been reported. Based on the available evidence, the inherited heterozygous c.5138G>A (p.Gly1713Asp) missense variant identified in the NALCN gene is reported as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: May 1, 2024