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

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Aug 17, 2021)
Last evaluated:
Apr 12, 2021
Accession:
VCV000357811.9
Variation ID:
357811
Description:
single nucleotide variant
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NM_001851.6(COL9A1):c.902C>T (p.Pro301Leu)

Allele ID
300947
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
6q13
Genomic location
6: 70281014 (GRCh38) GRCh38 UCSC
6: 70990717 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000006.11:g.70990717G>A
NC_000006.12:g.70281014G>A
NG_011654.1:g.27070C>T
... more HGVS
Protein change
P301L, P58L
Other names
-
Canonical SPDI
NC_000006.12:70281013:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00083
1000 Genomes Project 0.00060
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00079
The Genome Aggregation Database (gnomAD) 0.00150
The Genome Aggregation Database (gnomAD), exomes 0.00074
Exome Aggregation Consortium (ExAC) 0.00069
Trans-Omics for Precision Medicine (TOPMed) 0.00088
Trans-Omics for Precision Medicine (TOPMed) 0.00104
Links
ClinGen: CA3882594
dbSNP: rs192047082
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Apr 12, 2021 RCV001375076.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 21, 2020 RCV000991647.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL9A1 No evidence available No evidence available GRCh38
GRCh37
576 592

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Aug 31, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143285.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (1)
Likely benign
(Nov 10, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001197802.2
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Dec 21, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001763966.1
Submitted: (Aug 03, 2021)
Evidence details
Comment:
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 … (more)
Uncertain significance
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
Hearing impairment
Allele origin: germline
Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center
Accession: SCV001571893.2
Submitted: (Aug 17, 2021)
Evidence details
Comment:
PP3_Supporting

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Rare variants in CFI, C3 and C9 are associated with high risk of advanced age-related macular degeneration. Seddon JM Nature genetics 2013 PMID: 24036952

Text-mined citations for rs192047082...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021