Background: Alport syndrome (AS) and thin basement membrane nephropathy (TBMN) are heterogeneous renal hereditary diseases. Mutations of COL4A3 and COL4A4 genes were reported to be the underlying pathogenicity in both diseases. However, the mechanism of the same mutation causing totally different clinical processes and outcomes in AS and TBMN is still not clear. Subjects and Methods: Mutations of all coding exons of COL4A3 and COL4A4 were screened in a patient with autosomal recessive Alport syndrome (ARAS) of a Chinese Han consanguineous family by means of PCR and direct sequencing. Furthermore, the identified mutation was validated by restriction endonuclease AvaII in all 20 members in his family, as well as 46 patients with TBMN, 2 patients with AS from another two families, and 50 healthy controls. Results: A novel missense mutation (3725G>A, G1242D) in exon 42 of COL4A3 was identified in the proband in the homozygous form. This pathogenic mutation was demonstrated in all carriers who presented with hematuria or mild proteinuria in the heterozygous form, whereas it was not detected in others whose urinalysis was normal within the family. In addition, 10 polymorphisms, including 1 non-glycine missense variant and 9 neutral polymorphisms, were detected in COL4A3/COL4A4. Conclusion: The novel mutation (3725G>A, G1242D) of COL4A3 was the underlying pathogenic role in the homozygous form in ARAS and in the heterozygous form in TBMN within an identical family. The result provided a potentially useful clue for the functional investigation of COL4A3 in these two hereditary glomerular disorders.