COL4A4 G999E - GET-Evidence

Curation:
Currentness:

(See the latest version)

COL4A4 G999E

(COL4A4 Gly999Glu)


You are viewing an old version of this page that was saved on February 28, 2010 at 1:36pm by Madeleine Ball.

Edited in this revision:

Short summary

This variant is causative for Benign Familial Hematuria (thin membrane basement disease). While this variant is benign, it is useful in differentiating glomerular hematuria from Alport Syndrome.

Variant evidence
Computational 3

NBLOSUM=4, gene associated with disease, glycine mutations often causative for this disease.

See Wang YY et al. 2004 (14871398), unpublished research (below).

Functional -
Case/Control 2

OR=2

See Buzza M et al. 2003 (12631110).

Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Low clinical importance, Uncertain benign

(The "low clinical importance, uncertain" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

dominant

Summary of published research, and additional commentary

In the literature this variant was found associated with the phenotype in 3 symptomatic and one possibly symptomatic individual.

Allele frequency

  • T @ chr2:227915847: 1.0% (98/9708) in EVS
  • Frequency shown in summary reports: 1.0% (98/9708)

Publications
 

Buzza M, Dagher H, Wang YY, Wilson D, Babon JJ, Cotton RG, Savige J. Mutations in the COL4A4 gene in thin basement membrane disease. Kidney Int. 2003 Feb;63(2):447-53. PubMed PMID: 12631110.

In a screen for mutations in COL4A4 in 48 patients (of all ethnicities) with Thin Membrane Basement Disease, this variant was seen in 2 individuals. These patients were confirmed to not have Alport Syndrome. This variant was seen in 1/48 controls who did not have a renal biopsy, so they may not be actual controls. Glycine mutations in type IV collagen chains are often pathogenic, and pathogenicity cannot be excluded. The authors classify this as p. pathogenic. OR=2.

Wang YY, Rana K, Tonna S, Lin T, Sin L, Savige J. COL4A3 mutations and their clinical consequences in thin basement membrane nephropathy (TBMN). Kidney Int. 2004 Mar;65(3):786-90. PubMed PMID: 14871398.

In a screen for mutations in COL4A3 and the COL4A3/COL4A4 promoter in 62 patients (of unreported ethnicities) with Thin Membrane Basement Disease, this variant was seen in one 30yo female along with the “known mutation” COL4A3 G695R. The COL4A3 variants were not seen in 50 controls, but it is not clear if this variant was sampled. The authors report that glycine mutations are typically causative for disease, but the status of this variant is not clear.

Genomes
 

NA07022

 

snp-5

 

Other external references
 

    GeneTests
  • GeneTests records for the COL4A4 gene
    Collagen IV-Related Nephropathies (Alport Syndrome and Thin Base
    COL4A4 Alport Syndrome and Thin Basement Membrane Nephropathy
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/COL4A4
    Web search results (2 hits -- see all)
  • Amplified DNA Nanoarray Sequencing
    Human Genome Sequencing Using Unchained Base Reads on. Self-Assembling DNA Nanoarrays ... COL4A4. G999E. TBMD. G‐>E mutations are often causative in TBMD; possibly pathogenic in a ...
    www.sciencemag.org/cgi/data/1181498/DC1/1
  • Sup.doc
    This process incorporates several DNA engineering innovations to ... COL4A4. G999E. TBMD. G->E mutations are often causative in TBMD; possibly pathogenic in a ...
    arep.med.harvard.edu/pdf/Drmanac_sup_09.doc

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

Log in