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NM_006371.5(CRTAP):c.38C>A (p.Ala13Glu) AND Osteogenesis imperfecta type 7

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 13, 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:
RCV001206163.3

Allele description [Variation Report for NM_006371.5(CRTAP):c.38C>A (p.Ala13Glu)]

NM_006371.5(CRTAP):c.38C>A (p.Ala13Glu)

Genes:
LOC129936436:ATAC-STARR-seq lymphoblastoid silent region 14183 [Gene]
CRTAP:cartilage associated protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p22.3
Genomic location:
Preferred name:
NM_006371.5(CRTAP):c.38C>A (p.Ala13Glu)
HGVS:
  • NC_000003.12:g.33114115C>A
  • NG_008122.1:g.5158C>A
  • NM_006371.5:c.38C>AMANE SELECT
  • NP_006362.1:p.Ala13Glu
  • LRG_4t1:c.38C>A
  • LRG_4:g.5158C>A
  • NC_000003.11:g.33155607C>A
  • NC_000003.11:g.33155607C>A
  • NM_006371.4:c.38C>A
Protein change:
A13E
Links:
dbSNP: rs137853938
NCBI 1000 Genomes Browser:
rs137853938
Molecular consequence:
  • NM_006371.5:c.38C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Osteogenesis imperfecta type 7 (OI7)
Synonyms:
OI type 7; OI type VII; OSTEOGENESIS IMPERFECTA, TYPE IIB; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012536; MedGen: C1853162; OMIM: 610682

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001377459Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 13, 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

CRTAP mutations in lethal and severe osteogenesis imperfecta: the importance of combining biochemical and molecular genetic analysis.

Van Dijk FS, Nesbitt IM, Nikkels PG, Dalton A, Bongers EM, van de Kamp JM, Hilhorst-Hofstee Y, Den Hollander NS, Lachmeijer AM, Marcelis CL, Tan-Sindhunata GM, van Rijn RR, Meijers-Heijboer H, Cobben JM, Pals G.

Eur J Hum Genet. 2009 Dec;17(12):1560-9. doi: 10.1038/ejhg.2009.75. Epub 2009 Jun 24. Erratum in: Eur J Hum Genet. 2009 Dec;17(12):1692.

PubMed [citation]
PMID:
19550437
PMCID:
PMC2987020

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, SCV001377459.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 13 of the CRTAP protein (p.Ala13Glu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with osteogenesis imperfecta type III (PMID: 19550437). ClinVar contains an entry for this variant (Variation ID: 937198). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). 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.

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

Last Updated: Sep 29, 2024