COL9A1 S339P - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

COL9A1 S339P

(COL9A1 Ser339Pro)


Short summary

 

Variant evidence
Computational 2

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 1.00
GVGD: GV 73.35; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(1);
PolyPhen=benign(0);
Condel=not_computable_was(-1)
Mutation Tasting Prediction: Polymorphism, P value: 0.999995; protein features (might be) affected (aa 269-405 REGION Triple-helical region (COL3) gets lost)

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • G @ chr6:70984436: 47.9% (5153/10758) in EVS
  • G @ chr6:71041156: 59.4% (76/128) in GET-Evidence
  • Frequency shown in summary reports: 47.9% (5153/10758)

Publications
 

Genomes
 

 

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom G @ chr6:70984436

 

 

 

 

 

 

 

 

 

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het G @ chr6:70984436

 

 

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het G @ chr6:70984436

 

 

 

 

 

 

 

 

 

 

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
hom G @ chr6:70984436

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het G @ chr6:70984436

 

 

 

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het G @ chr6:70984436

 

GS06985 - var-GS06985-1100-36-ASM
het G @ chr6:71041157

 

GS06994 - var-GS06994-1100-36-ASM
het G @ chr6:71041157

 

GS07357 - var-GS07357-1100-36-ASM
het G @ chr6:71041157

 

GS10851 - var-GS10851-1100-36-ASM
hom G @ chr6:71041157

 

GS12004 - var-GS12004-1100-36-ASM
hom G @ chr6:71041157

 

GS18501 - var-GS18501-1100-36-ASM
hom G @ chr6:71041157

 

GS18502 - var-GS18502-1100-36-ASM
het G @ chr6:71041157

 

GS18504 - var-GS18504-1100-36-ASM
het G @ chr6:71041157

 

GS18505 - var-GS18505-1100-36-ASM
hom G @ chr6:71041157

 

GS18508 - var-GS18508-1100-36-ASM
hom G @ chr6:71041157

 

GS18517 - var-GS18517-1100-36-ASM
hom G @ chr6:71041157

 

GS18537 - var-GS18537-1100-36-ASM
hom G @ chr6:71041157

 

GS18555 - var-GS18555-1100-36-ASM
hom G @ chr6:71041157

 

GS18947 - var-GS18947-1100-36-ASM
hom G @ chr6:71041157

 

GS18956 - var-GS18956-1100-36-ASM
hom G @ chr6:71041157

 

GS19017 - var-GS19017-1100-36-ASM
hom G @ chr6:71041157

 

GS19020 - var-GS19020-1100-36-ASM
het G @ chr6:71041157

 

GS19025 - var-GS19025-1100-36-ASM
hom G @ chr6:71041157

 

GS19026 - var-GS19026-1100-36-ASM
hom G @ chr6:71041157

 

GS19129 - var-GS19129-1100-36-ASM
hom G @ chr6:71041157

 

GS19238 - var-GS19238-1100-36-ASM
hom G @ chr6:71041157

 

GS19239 - var-GS19239-1100-36-ASM
het G @ chr6:71041157

 

GS19240 - var-GS19240-1100-36-ASM
hom G @ chr6:71041157

 

GS19648 - var-GS19648-1100-36-ASM
het G @ chr6:71041157

 

GS19670 - var-GS19670-1100-36-ASM
het G @ chr6:71041157

 

GS19700 - var-GS19700-1100-36-ASM
hom G @ chr6:71041157

 

GS19701 - var-GS19701-1100-36-ASM
hom G @ chr6:71041157

 

GS19704 - var-GS19704-1100-36-ASM
het G @ chr6:71041157

 

GS19735 - var-GS19735-1100-36-ASM
het G @ chr6:71041157

 

GS19834 - var-GS19834-1100-36-ASM
hom G @ chr6:71041157

 

GS20509 - var-GS20509-1100-36-ASM
hom G @ chr6:71041157

 

GS21767 - var-GS21767-1100-36-ASM
het G @ chr6:71041157

 

Other external references
 

    dbSNP
  • rs592121
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the COL9A1 gene
    Stickler Syndrome
    COL9A1-Related Multiple Epiphyseal Dysplasia
    COL9A1-Related Stickler Syndrome
    Multiple Epiphyseal Dysplasia, Dominant
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL9A1
    Web search results (12 hits -- see all)
  • A Mutation in COL9A1 Causes Multiple Epiphyseal Dysplasia ...
    Recombination was observed between COL9A1, COL9A2, COL9A3, and COMP ... Screening of COL9A1 for mutations in the two probands from the families ...
    sciencedirect.com/science?_ob=MImg&...&ie=/sdarticle.pdf
  • Type I- 99%
    ... rs17853288) 15489334 FANCM Q8IYD8 S175F 175 VAR_023697 PKC (0.977) ... IKK (0.781) Polymorphism (dbSNP:rs12360890) COL9A1 P20849 S339P 339 VAR_026463 CK1 (0.745) 11565064 CDK2 ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_99.txt
  • Type II- 95%
    ... SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID Removed ... P80365 R186C 184 VAR_015637 PKC (0.550) AME 7593417 9661590 PKLR P30613 D390N ...
    nih.go.kr/phosphovariant/html/family_whole/TypeII-_95.txt

Other in silico analyses
 

  • NBLOSUM100 score = 3
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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