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Whole exome sequencing reveals novel COL4A3 and COL4A4 mutations and resolves diagnosis in Chinese families with kidney disease.

Lin F, Bian F, Zou J, Wu X, Shan J, Lu W, Yao Y, Jiang G, Gale DP - BMC Nephrol (2014)

Bottom Line: COL4A4 c.C4715T has previously been associated with autosomal recessive AS and was inherited from his clinically unaffected father.In family 3, ESRD occurred in both male and females who were found to harbor a known AS-causing COL4A5 donor splice site mutation (c.687+1G>A).WES identified 2 novel and 2 known pathogenic COL4A3/COL4A4/COL4A5 mutations in 3 families with previously unexplained inherited kidney disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Nephrology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. jianggeng-ru@hotmail.com.

ABSTRACT

Background: Collagen IV-related nephropathies, including thin basement membrane nephropathy and Alport Syndrome (AS), are caused by defects in the genes COL4A3, COL4A4 and COL4A5. Diagnosis of these conditions can be hindered by variable penetrance and the presence of non-specific clinical or pathological features.

Methods: Three families with unexplained inherited kidney disease were recruited from Shanghai, China. Whole exome sequencing (WES) was performed in the index case from each family and co-segregation of candidate pathogenic mutations was tested by Sanger sequencing.

Results: We identified COL4A4 missense variants [c.G2636A (p.Gly879Glu) and c.C4715T (p.Pro1572Leu)] in the 21-year-old male proband from family 1, who had been diagnosed with mesangial proliferative nephropathy at age 14. COL4A4 c.G2636A, a novel variant, co-segregated with renal disease among maternal relatives. COL4A4 c.C4715T has previously been associated with autosomal recessive AS and was inherited from his clinically unaffected father. In family 2, a novel COL4A3 missense mutation c.G2290A (p.Gly997Glu) was identified in a 45-year-old male diagnosed with focal segmental glomerulosclerosis and was present in all his affected family members, who exhibited disease ranging from isolated microscopic hematuria to end stage renal disease (ESRD). In family 3, ESRD occurred in both male and females who were found to harbor a known AS-causing COL4A5 donor splice site mutation (c.687+1G>A). None of these variants were detected among 100 healthy Chinese individuals.

Conclusion: WES identified 2 novel and 2 known pathogenic COL4A3/COL4A4/COL4A5 mutations in 3 families with previously unexplained inherited kidney disease. These findings highlight the clinical range of collagen IV-related nephropathies and resolved diagnostic confusion arising from atypical or incomplete clinical/histological findings, allowing appropriate counselling and treatment advice to be given.

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Overview of theCOL4A5mutation identified in Family 3. (A) Pedigree for family 3. A full-shaded icon denotes ESRD; a 3/4-shaded icon denotes impaired renal function; individual with unknown phenotype is indicated in gray. Asterisk indicates the individual examined by whole exome sequencing. (B) Sanger sequencing electropherograms confirming the COL4A5 donor splice site mutation (c.687 + 1G > A), and multiple species sequence alignment showing conserved GT in the donor splice site.
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Fig4: Overview of theCOL4A5mutation identified in Family 3. (A) Pedigree for family 3. A full-shaded icon denotes ESRD; a 3/4-shaded icon denotes impaired renal function; individual with unknown phenotype is indicated in gray. Asterisk indicates the individual examined by whole exome sequencing. (B) Sanger sequencing electropherograms confirming the COL4A5 donor splice site mutation (c.687 + 1G > A), and multiple species sequence alignment showing conserved GT in the donor splice site.

Mentions: Whole exome sequencing was performed in II-2. After variant filtering, we identified a COL4A5 donor splice site variant (c.687 + 1G > A), which was previously reported to cause XLAS [20], and a rare heterozygous CUBN missense mutation [c.C9206T (p.Thr3069Ile)] with MAF of 0.003 (Figure 4A). Sanger sequencing (Figure 4B) confirmed that COL4A5 (c.687 + 1G > A) cosegregated in all affected members in this family while the CUBN variant was not present in affected individuals II-3 and III-2, and was present in clinically unaffected individuals II-7 and III-3 (results summarized in Table 1). Sanger sequencing confirmed that COL4A5 (c.687 + 1G > A) was not present in 100 healthy Chinese controls.Figure 4


Whole exome sequencing reveals novel COL4A3 and COL4A4 mutations and resolves diagnosis in Chinese families with kidney disease.

Lin F, Bian F, Zou J, Wu X, Shan J, Lu W, Yao Y, Jiang G, Gale DP - BMC Nephrol (2014)

Overview of theCOL4A5mutation identified in Family 3. (A) Pedigree for family 3. A full-shaded icon denotes ESRD; a 3/4-shaded icon denotes impaired renal function; individual with unknown phenotype is indicated in gray. Asterisk indicates the individual examined by whole exome sequencing. (B) Sanger sequencing electropherograms confirming the COL4A5 donor splice site mutation (c.687 + 1G > A), and multiple species sequence alignment showing conserved GT in the donor splice site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4233041&req=5

Fig4: Overview of theCOL4A5mutation identified in Family 3. (A) Pedigree for family 3. A full-shaded icon denotes ESRD; a 3/4-shaded icon denotes impaired renal function; individual with unknown phenotype is indicated in gray. Asterisk indicates the individual examined by whole exome sequencing. (B) Sanger sequencing electropherograms confirming the COL4A5 donor splice site mutation (c.687 + 1G > A), and multiple species sequence alignment showing conserved GT in the donor splice site.
Mentions: Whole exome sequencing was performed in II-2. After variant filtering, we identified a COL4A5 donor splice site variant (c.687 + 1G > A), which was previously reported to cause XLAS [20], and a rare heterozygous CUBN missense mutation [c.C9206T (p.Thr3069Ile)] with MAF of 0.003 (Figure 4A). Sanger sequencing (Figure 4B) confirmed that COL4A5 (c.687 + 1G > A) cosegregated in all affected members in this family while the CUBN variant was not present in affected individuals II-3 and III-2, and was present in clinically unaffected individuals II-7 and III-3 (results summarized in Table 1). Sanger sequencing confirmed that COL4A5 (c.687 + 1G > A) was not present in 100 healthy Chinese controls.Figure 4

Bottom Line: COL4A4 c.C4715T has previously been associated with autosomal recessive AS and was inherited from his clinically unaffected father.In family 3, ESRD occurred in both male and females who were found to harbor a known AS-causing COL4A5 donor splice site mutation (c.687+1G>A).WES identified 2 novel and 2 known pathogenic COL4A3/COL4A4/COL4A5 mutations in 3 families with previously unexplained inherited kidney disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Nephrology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. jianggeng-ru@hotmail.com.

ABSTRACT

Background: Collagen IV-related nephropathies, including thin basement membrane nephropathy and Alport Syndrome (AS), are caused by defects in the genes COL4A3, COL4A4 and COL4A5. Diagnosis of these conditions can be hindered by variable penetrance and the presence of non-specific clinical or pathological features.

Methods: Three families with unexplained inherited kidney disease were recruited from Shanghai, China. Whole exome sequencing (WES) was performed in the index case from each family and co-segregation of candidate pathogenic mutations was tested by Sanger sequencing.

Results: We identified COL4A4 missense variants [c.G2636A (p.Gly879Glu) and c.C4715T (p.Pro1572Leu)] in the 21-year-old male proband from family 1, who had been diagnosed with mesangial proliferative nephropathy at age 14. COL4A4 c.G2636A, a novel variant, co-segregated with renal disease among maternal relatives. COL4A4 c.C4715T has previously been associated with autosomal recessive AS and was inherited from his clinically unaffected father. In family 2, a novel COL4A3 missense mutation c.G2290A (p.Gly997Glu) was identified in a 45-year-old male diagnosed with focal segmental glomerulosclerosis and was present in all his affected family members, who exhibited disease ranging from isolated microscopic hematuria to end stage renal disease (ESRD). In family 3, ESRD occurred in both male and females who were found to harbor a known AS-causing COL4A5 donor splice site mutation (c.687+1G>A). None of these variants were detected among 100 healthy Chinese individuals.

Conclusion: WES identified 2 novel and 2 known pathogenic COL4A3/COL4A4/COL4A5 mutations in 3 families with previously unexplained inherited kidney disease. These findings highlight the clinical range of collagen IV-related nephropathies and resolved diagnostic confusion arising from atypical or incomplete clinical/histological findings, allowing appropriate counselling and treatment advice to be given.

Show MeSH
Related in: MedlinePlus