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NM_000088.4(COL1A1):c.865C>T (p.Pro289Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 27, 2017
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:
RCV000431408.1

Allele description [Variation Report for NM_000088.4(COL1A1):c.865C>T (p.Pro289Ser)]

NM_000088.4(COL1A1):c.865C>T (p.Pro289Ser)

Genes:
LOC126862586:CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:48273702-48274901 [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.865C>T (p.Pro289Ser)
HGVS:
  • NC_000017.11:g.50196522G>A
  • NG_007400.1:g.10118C>T
  • NM_000088.4:c.865C>TMANE SELECT
  • NP_000079.2:p.Pro289Ser
  • NP_000079.2:p.Pro289Ser
  • LRG_1t1:c.865C>T
  • LRG_1:g.10118C>T
  • LRG_1p1:p.Pro289Ser
  • NC_000017.10:g.48273883G>A
  • NM_000088.3:c.865C>T
Protein change:
P289S
Links:
dbSNP: rs1057524833
NCBI 1000 Genomes Browser:
rs1057524833
Molecular consequence:
  • NM_000088.4:c.865C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000536576GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 27, 2017) 		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, SCV000536576.3

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

Description

The P289S variant in the COL1A1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The P289S variant was not observed in approximately 6500 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 P289S variant is a non-conservative amino acid substitution, which occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret P289S as a variant of uncertain significance

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

Last Updated: Mar 26, 2023