COL4A3 G43R - GET-Evidence

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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.

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Curation:
Currentness:

COL4A3 G43R

(COL4A3 Gly43Arg)


Short summary

 

Variant evidence
Computational 4

PolyPhen: Probably damaging 0.999
SIFT: Affect protein function 0.00
GVGD: GV 0.00; GD 125.13; Class C65
Variant Effect Predictor (Ensembl ):
SIFT=deleterious(0.01);
PolyPhen=unknown(0)
Mutation Tasting Prediction: Polymorphism, P value: 0.055257; protein features (might be) affected (aa 43-1438 Triple-helical region 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

  • C @ chr2:228102723: 35.3% (3381/9580) in EVS
  • C @ chr2:227810966: 28.6% (36/126) in GET-Evidence
  • Frequency shown in summary reports: 35.3% (3381/9580)

Publications
 

Genomes
 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het C @ chr2:228102723

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het C @ chr2:228102723

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het C @ chr2:228102723

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het C @ chr2:228102723

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
het C @ chr2:227810967

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom C @ chr2:228102723

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het C @ chr2:228102723

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het C @ chr2:227810967

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het C @ chr2:228102723

 

hu3A8D13 - PGP13 (hu3A8D13) build 37, from CGI var (software ver 1.11.0.16), CGI sample GS000003289
het C @ chr2:228102723

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het C @ chr2:228102723

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het C @ chr2:228102723

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het C @ chr2:228102723

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
hom C @ chr2:228102723

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
hom C @ chr2:228102723

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het C @ chr2:228102723

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het C @ chr2:227810967

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het C @ chr2:228102723

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het C @ chr2:228102723

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
hom C @ chr2:228102723

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
het C @ chr2:228102723

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het C @ chr2:228102723

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het C @ chr2:228102723

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het C @ chr2:228102723

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het C @ chr2:228102723

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het C @ chr2:228102723

 

GS10851 - var-GS10851-1100-36-ASM
het C @ chr2:227810967

 

GS12004 - var-GS12004-1100-36-ASM
het C @ chr2:227810967

 

GS18505 - var-GS18505-1100-36-ASM
het C @ chr2:227810967

 

GS18508 - var-GS18508-1100-36-ASM
hom C @ chr2:227810967

 

GS18517 - var-GS18517-1100-36-ASM
het C @ chr2:227810967

 

GS18940 - var-GS18940-1100-36-ASM
hom C @ chr2:227810967

 

GS18942 - var-GS18942-1100-36-ASM
hom C @ chr2:227810967

 

GS19017 - var-GS19017-1100-36-ASM
het C @ chr2:227810967

 

GS19025 - var-GS19025-1100-36-ASM
het C @ chr2:227810967

 

GS19239 - var-GS19239-1100-36-ASM
hom C @ chr2:227810967

 

GS19240 - var-GS19240-1100-36-ASM
het C @ chr2:227810967

 

GS19648 - var-GS19648-1100-36-ASM
hom C @ chr2:227810967

 

GS19649 - var-GS19649-1100-36-ASM
het C @ chr2:227810967

 

GS19669 - var-GS19669-1100-36-ASM
het C @ chr2:227810967

 

GS19700 - var-GS19700-1100-36-ASM
hom C @ chr2:227810967

 

GS19704 - var-GS19704-1100-36-ASM
hom C @ chr2:227810967

 

GS20509 - var-GS20509-1100-36-ASM
het C @ chr2:227810967

 

GS21767 - var-GS21767-1100-36-ASM
hom C @ chr2:227810967

 

NA12878

 

Other external references
 

    dbSNP
  • rs13424243
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the COL4A3 gene
    Collagen IV-Related Nephropathies (Alport Syndrome and Thin Base
    COL4A3 Alport Syndrome and Thin Basement Membrane Nephropathy
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL4A3
    Web search results (25 hits -- see all)
  • Molecular Vision: Polymorphisms in COL4A3 and COL4A4 genes ...
    Polymorphisms in COL4A3 and COL4A4 genes associated with keratoconus ... SIFT tool analysis gave a score less than 0.05 for G43R in COL4A3 and G545A in COL4A4. ...
    www.molvis.org/molvis/v15/a301
  • Mutations in the COL4A4 and COL4A3 Genes Cause Familial ...
    type analysis showed that linkage to the COL4A3/4 locus could ... polymorphisms in the COL4A3 (G43R) and. COL4A4 genes (G545A) (22,23). G43R is supposed to ...
    jasn.asnjournals.org/cgi/reprint/13/5/1248.pdf
  • Kidney International - COL4A3/COL4A4 mutations: From familial ...
    COL4A3/COL4A4 mutations: From familial hematuria to autosomal-dominant or recessive ... common non-pathogenic polymorphisms: G43R in COL4A310 and G545A in ...
    www.nature.com/ki/journal/v61/n6/full/4492973a.html
  • Structure of the Human Type IV Collagen Gene COL4A3 and ...
    Reported here are the complete COL4A3 exon-intron structure and a comprehensive ... The frequency of the G43R variant allele in controls (42%) excluded the ...
    jasn.asnjournals.org/cgi/content/full/12/1/97
  • Supplementary Table xls.1
    ... kÇkükékâkäkàkåkçkêkëkèkïkîkìkÄkÅkÉkækÆkôkökòkûkùkÿkÖkÜk¢k£k¥k₧kƒkákíkókúkñkÑkªkºk¿kk¬k½k ... 0_-;_-"ú"* "-"_-;_-@0_-;\-* #,##0_-;_-* "-"_-;8_-"ú"* #,##0.00_-;\-"ú" ...
    icr.ac.uk/research/research_sections/.../2843.xls
  • Polymorphisms in COL4A3 and COL4A4 genes associated with ...
    significance of alterations in COL4A3 and COL4A4 genes in KC patients, we ... that G43R, P141L, D326Y, and P574L polymorphisms in the. COL4A3 gene are potentially ...
    www.molvis.org/molvis/v15/a301/mv-v15-a301-stabuc-silih.pdf

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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