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NM_000088.4(COL1A1):c.1375C>A (p.Pro459Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 10, 2016
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:
RCV000422156.1

Allele description [Variation Report for NM_000088.4(COL1A1):c.1375C>A (p.Pro459Thr)]

NM_000088.4(COL1A1):c.1375C>A (p.Pro459Thr)

Gene:
COL1A1:collagen type I alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.33
Genomic location:
Preferred name:
NM_000088.4(COL1A1):c.1375C>A (p.Pro459Thr)
HGVS:
  • NC_000017.11:g.50194807G>T
  • NG_007400.1:g.11833C>A
  • NM_000088.4:c.1375C>AMANE SELECT
  • NP_000079.2:p.Pro459Thr
  • NP_000079.2:p.Pro459Thr
  • LRG_1t1:c.1375C>A
  • LRG_1:g.11833C>A
  • LRG_1p1:p.Pro459Thr
  • NC_000017.10:g.48272168G>T
  • NM_000088.3:c.1375C>A
Protein change:
P459T
Links:
dbSNP: rs751299130
NCBI 1000 Genomes Browser:
rs751299130
Molecular consequence:
  • NM_000088.4:c.1375C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000530770GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Aug 10, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000530770.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The P459T variant in the COL1A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The P459T variant was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The P459T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret P459T as a variant of uncertain significance.

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

Last Updated: Sep 29, 2024