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NM_001851.6(COL9A1):c.902C>T (p.Pro301Leu) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 14, 2024
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:
RCV004767244.1

Allele description [Variation Report for NM_001851.6(COL9A1):c.902C>T (p.Pro301Leu)]

NM_001851.6(COL9A1):c.902C>T (p.Pro301Leu)

Gene:
COL9A1:collagen type IX alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6q13
Genomic location:
Preferred name:
NM_001851.6(COL9A1):c.902C>T (p.Pro301Leu)
HGVS:
  • NC_000006.12:g.70281014G>A
  • NG_011654.1:g.27070C>T
  • NM_001377289.1:c.173C>T
  • NM_001377290.1:c.173C>T
  • NM_001377291.1:c.902C>T
  • NM_001851.6:c.902C>TMANE SELECT
  • NM_078485.4:c.173C>T
  • NP_001364218.1:p.Pro58Leu
  • NP_001364219.1:p.Pro58Leu
  • NP_001364220.1:p.Pro301Leu
  • NP_001842.3:p.Pro301Leu
  • NP_511040.2:p.Pro58Leu
  • NC_000006.11:g.70990717G>A
  • NM_001851.4:c.902C>T
  • NR_165185.1:n.318C>T
Protein change:
P301L
Links:
dbSNP: rs192047082
NCBI 1000 Genomes Browser:
rs192047082
Molecular consequence:
  • NM_001377289.1:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377290.1:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001377291.1:c.902C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001851.6:c.902C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_078485.4:c.173C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_165185.1:n.318C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005381132Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Aug 14, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005381132.1

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

Description

Variant summary: COL9A1 c.902C>T (p.Pro301Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00074 in 246936 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in COL9A1 causing COL9A1-Related Disorders, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.902C>T in individuals affected with COL9A1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 357811). Based on the evidence outlined above, the variant was classified as uncertain significance.

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

Last Updated: Nov 10, 2024