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NM_052867.4(NALCN):c.3542G>A (p.Arg1181Gln) AND Congenital contractures of the limbs and face, hypotonia, and developmental delay

Germline classification:
Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:
Nov 7, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000224736.7

Allele description [Variation Report for NM_052867.4(NALCN):c.3542G>A (p.Arg1181Gln)]

NM_052867.4(NALCN):c.3542G>A (p.Arg1181Gln)

Gene:
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.3542G>A (p.Arg1181Gln)
HGVS:
  • NC_000013.11:g.101083752C>T
  • NG_053176.1:g.338455G>A
  • NM_001350748.2:c.3629G>A
  • NM_001350749.2:c.3542G>A
  • NM_001350750.2:c.3455G>A
  • NM_001350751.2:c.3455G>A
  • NM_052867.4:c.3542G>AMANE SELECT
  • NP_001337677.1:p.Arg1210Gln
  • NP_001337678.1:p.Arg1181Gln
  • NP_001337679.1:p.Arg1152Gln
  • NP_001337680.1:p.Arg1152Gln
  • NP_443099.1:p.Arg1181Gln
  • NC_000013.10:g.101736103C>T
  • NM_052867.2:c.3542G>A
  • Q8IZF0:p.Arg1181Gln
Protein change:
R1152Q
Links:
UniProtKB: Q8IZF0#VAR_076678; dbSNP: rs786201003
NCBI 1000 Genomes Browser:
rs786201003
Molecular consequence:
  • NM_001350748.2:c.3629G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350749.2:c.3542G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350750.2:c.3455G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001350751.2:c.3455G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_052867.4:c.3542G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000281697University of Washington Center for Mendelian Genomics, University of Washington
no assertion criteria provided
Pathogenic
(May 19, 2015)
de novoresearch

PubMed (1)
[See all records that cite this PMID]

SCV000599270Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 13, 2016)
de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004045798Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)
Likely pathogenic
(Nov 7, 2022)
de novoclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot providednot providednot providedclinical testing, research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

De novo mutations in NALCN cause a syndrome characterized by congenital contractures of the limbs and face, hypotonia, and developmental delay.

Chong JX, McMillin MJ, Shively KM, Beck AE, Marvin CT, Armenteros JR, Buckingham KJ, Nkinsi NT, Boyle EA, Berry MN, Bocian M, Foulds N, Uzielli ML, Haldeman-Englert C, Hennekam RC, Kaplan P, Kline AD, Mercer CL, Nowaczyk MJ, Klein Wassink-Ruiter JS, McPherson EW, Moreno RA, et al.

Am J Hum Genet. 2015 Mar 5;96(3):462-73. doi: 10.1016/j.ajhg.2015.01.003. Epub 2015 Feb 12.

PubMed [citation]
PMID:
25683120
PMCID:
PMC4375444

Details of each submission

From University of Washington Center for Mendelian Genomics, University of Washington, SCV000281697.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals, SCV000599270.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV004045798.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024