NM_052867.4(NALCN):c.883del (p.Arg295fs) AND Congenital contractures of the limbs and face, hypotonia, and developmental delay

Germline classification:: Likely pathogenic (1 submission)
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:: RCV001250195.2

Allele description [Variation Report for NM_052867.4(NALCN):c.883del (p.Arg295fs)]

NM_052867.4(NALCN):c.883del (p.Arg295fs)

Gene:

NALCN:sodium leak channel, non-selective [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q33.1

Genomic location:

Preferred name:

NM_052867.4(NALCN):c.883del (p.Arg295fs)

HGVS:

NC_000013.11:g.101292283del
NC_000013.11:g.101292286del
NG_053176.1:g.129924del
NM_001350748.2:c.883del
NM_001350749.2:c.883del
NM_001350750.2:c.883del
NM_001350751.2:c.883del
NM_052867.4:c.883delMANE SELECT
NP_001337677.1:p.Arg295fs
NP_001337678.1:p.Arg295fs
NP_001337679.1:p.Arg295fs
NP_001337680.1:p.Arg295fs
NP_443099.1:p.Arg295fs
NC_000013.10:g.101944637del
NM_001350748.1:c.883del

Protein change:

R295fs

Links:

dbSNP: rs2043584001

NCBI 1000 Genomes Browser:

rs2043584001

Molecular consequence:

NM_001350748.2:c.883del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001350749.2:c.883del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001350750.2:c.883del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001350751.2:c.883del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_052867.4:c.883del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD)
Identifiers:: MONDO: MONDO:0014556; MedGen: C4225398; OMIM: 616266

Recent activity

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recombining binding protein suppressor of hairless isoform X1 [Rattus norvegicus...
recombining binding protein suppressor of hairless isoform X1 [Rattus norvegicus]
gi|2678896453|ref|XP_063129654.1|

Protein
PREDICTED: Rattus norvegicus recombination signal binding protein for immunoglob...
PREDICTED: Rattus norvegicus recombination signal binding protein for immunoglobulin kappa J region (Rbpj), transcript variant X1, mRNA
gi|2678896452|ref|XM_063273584.1|

Nucleotide
ankyrin repeat and EF-hand domain containing 1a [Danio rerio]
ankyrin repeat and EF-hand domain containing 1a [Danio rerio]
gi|70887735|ref|NP_001020714.1|

Protein
multiple C2 and transmembrane domain-containing protein 1 isoform X2 [Danio reri...
multiple C2 and transmembrane domain-containing protein 1 isoform X2 [Danio rerio]
gi|2800590037|ref|XP_068077619.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001424461	Centogene AG - the Rare Disease Company	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001424461

Centogene AG - the Rare Disease Company

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

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

Details of each submission

From Centogene AG - the Rare Disease Company, SCV001424461.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 7, 2023

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