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NM_002526.4(NT5E):c.1608dup (p.Val537fs) AND NT5E-related condition

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 11, 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:
RCV003407354.4

Allele description

NM_002526.4(NT5E):c.1608dup (p.Val537fs)

Gene:
NT5E:5'-nucleotidase ecto [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
6q14.3
Genomic location:
Preferred name:
NM_002526.4(NT5E):c.1608dup (p.Val537fs)
HGVS:
  • NC_000006.12:g.85493887dup
  • NG_028214.1:g.49304dup
  • NM_001204813.2:c.1458dup
  • NM_002526.4:c.1608dupMANE SELECT
  • NP_001191742.1:p.Val487fs
  • NP_002517.1:p.Val537fs
  • NC_000006.11:g.86203605dup
  • NM_002526.3:c.1608dupA
Note:
ClinGen staff contributed the HGVS expression for this variant.
Protein change:
V487fs
Links:
OMIM: 129190.0003; dbSNP: rs774200574
NCBI 1000 Genomes Browser:
rs774200574
Molecular consequence:
  • NM_001204813.2:c.1458dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002526.4:c.1608dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
NT5E-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004113489PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jul 11, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004113489.1

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

Description

The NT5E c.1608dupA variant is predicted to result in a frameshift and premature protein termination (p.Val537Serfs*7). This variant was reported in the compound heterozygous state and homozygous state in two unrelated individuals with arterial and joint calcifications (Family 3, Figure 1B, St Hilaire et al. 2011. PubMed ID: 21288095; Figure 2, Avruscio et al. 2020. PubMed ID: 32532917). In vitro experimental studies suggest this variant impacts protein function (Figure 2F, St Hilaire et al 2011. PubMed ID: 21288095; Fausther et al. 2014. PubMed ID: 24887587). This variant is reported in 0.017% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/6-86203602-G-GA). Frameshift variants in NT5E are expected to be pathogenic. Of note, this variant resides in the final exon of this gene, and it is unclear if the resulting mRNA would undergo nonsense-mediated decay. This variant is interpreted as likely pathogenic.

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

Last Updated: Mar 10, 2024