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NM_001287.6(CLCN7):c.739-18G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 20, 2023
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:
RCV001859278.3

Allele description

NM_001287.6(CLCN7):c.739-18G>A

Gene:
CLCN7:chloride voltage-gated channel 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_001287.6(CLCN7):c.739-18G>A
HGVS:
  • NC_000016.10:g.1457355C>T
  • NG_007567.1:g.22730G>A
  • NM_001114331.3:c.667-18G>A
  • NM_001287.6:c.739-18G>AMANE SELECT
  • NC_000016.9:g.1507356C>T
  • NM_001287.5:c.739-18G>A
Links:
dbSNP: rs371893553
NCBI 1000 Genomes Browser:
rs371893553
Molecular consequence:
  • NM_001114331.3:c.667-18G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001287.6:c.739-18G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002143128Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 20, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Expanding the phenome and variome of skeletal dysplasia.

Maddirevula S, Alsahli S, Alhabeeb L, Patel N, Alzahrani F, Shamseldin HE, Anazi S, Ewida N, Alsaif HS, Mohamed JY, Alazami AM, Ibrahim N, Abdulwahab F, Hashem M, Abouelhoda M, Monies D, Al Tassan N, Alshammari M, Alsagheir A, Seidahmed MZ, Sogati S, Aglan MS, et al.

Genet Med. 2018 Dec;20(12):1609-1616. doi: 10.1038/gim.2018.50. Epub 2018 Apr 5.

PubMed [citation]
PMID:
29620724

Successful application of genome sequencing in a diagnostic setting: 1007 index cases from a clinically heterogeneous cohort.

Bertoli-Avella AM, Beetz C, Ameziane N, Rocha ME, Guatibonza P, Pereira C, Calvo M, Herrera-Ordonez N, Segura-Castel M, Diego-Alvarez D, Zawada M, Kandaswamy KK, Werber M, Paknia O, Zielske S, Ugrinovski D, Warnack G, Kampe K, Iurașcu MI, Cozma C, Vogel F, Alhashem A, et al.

Eur J Hum Genet. 2021 Jan;29(1):141-153. doi: 10.1038/s41431-020-00713-9. Epub 2020 Aug 28.

PubMed [citation]
PMID:
32860008
PMCID:
PMC7852664
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002143128.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant has been observed in individual(s) with clinical features of autosomal recessive osteopetrosis (PMID: 29620724, 32552793, 32860008; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs371893553, gnomAD 0.008%). This sequence change falls in intron 8 of the CLCN7 gene. It does not directly change the encoded amino acid sequence of the CLCN7 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Studies have shown that this variant results in retention of part of intron 8 and introduces a premature termination codon (PMID: 32552793). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 1029299).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 4, 2024