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

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(2) (Last evaluated: Dec 21, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000991647.5

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)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001143285Athena Diagnostics Inccriteria provided, single submitter
Uncertain significance
(Aug 31, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001197802Invitaecriteria provided, single submitter
Likely benign
(Nov 10, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001763966GeneDxcriteria provided, single submitter
Uncertain significance
(Dec 21, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration.

Seddon JM, Yu Y, Miller EC, Reynolds R, Tan PL, Gowrisankar S, Goldstein JI, Triebwasser M, Anderson HE, Zerbib J, Kavanagh D, Souied E, Katsanis N, Daly MJ, Atkinson JP, Raychaudhuri S.

Nat Genet. 2013 Nov;45(11):1366-70. doi: 10.1038/ng.2741. Epub 2013 Sep 15.

PubMed [citation]
PMID:
24036952
PMCID:
PMC3902040

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317
See all PubMed Citations (3)

Details of each submission

From Athena Diagnostics Inc, SCV001143285.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001197802.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001763966.1

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

Description

Previously reported in a female with infantile malignant osteopetrosis who also harbored a homozygous frameshift variant in the TCIRG1 gene (Zhang et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in ClinVar (ClinVar Variant ID# 357811; Landrum et al., 2016)

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

Last Updated: Nov 20, 2021

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