NM_014208.3(DSPP):c.53T>C (p.Val18Ala) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 1, 2022
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:
RCV003682906.2

Allele description [Variation Report for NM_014208.3(DSPP):c.53T>C (p.Val18Ala)]

NM_014208.3(DSPP):c.53T>C (p.Val18Ala)

Gene:
DSPP:dentin sialophosphoprotein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4q22.1
Genomic location:
Preferred name:
NM_014208.3(DSPP):c.53T>C (p.Val18Ala)
HGVS:
  • NC_000004.12:g.87612106T>C
  • NG_011595.1:g.8578T>C
  • NM_014208.3:c.53T>CMANE SELECT
  • NP_055023.2:p.Val18Ala
  • LRG_1242t1:c.53T>C
  • LRG_1242:g.8578T>C
  • LRG_1242p1:p.Val18Ala
  • NC_000004.11:g.88533258T>C
Protein change:
V18A
Molecular consequence:
  • NM_014208.3:c.53T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004408968Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 1, 2022) 		germlineclinical testing

PubMed (2)
[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

A novel mutation in the DSPP gene associated with dentinogenesis imperfecta type II.

Lee SK, Lee KE, Jeon D, Lee G, Lee H, Shin CU, Jung YJ, Lee SH, Hahn SH, Kim JW.

J Dent Res. 2009 Jan;88(1):51-5. doi: 10.1177/0022034508328168.

PubMed [citation]
PMID:
19131317

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004408968.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant disrupts the p.Val18 amino acid residue in DSPP. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 19131317). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with DSPP-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 18 of the DSPP protein (p.Val18Ala).

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

Last Updated: Sep 29, 2024