BackgroundCohen syndrome is a multisystem autosomal recessive hereditary disease, which is caused by variants of the VPS13B gene. The clinical manifestations include characteristic facial features, microcephaly, trunk obesity and mental retardation. The SLC26A4 gene encodes an anion transporter called Pendrin, the variants of SLC26A4 lead to deafness, Pendred syndrome and enlarged vestibular aqueduct. We presence a case of multiple genetic homozygous variants of SLC26A4 and VPS13B.Case presentationIn this study, we described a case of a 65-day-old female infant presenting with hearing loss and poor feeding. The deafness gene screening before admission showed that the patient carried homozygous c.919-2A>G variation of SLC26A4 gene. The symptoms of the patient did not improve significantly after a period of targeted treatment, then the possibility of genetic diseases was considered after consultation with the different departments. Whole exome sequencing was performed, and homozygous splicing variants in intron 38 (c.6940+1G>T) of VPS13B and that in intron 7 (c.919-2A>G) of SLC26A4 were identified. Later, the parent was proved as the carriers of VPS13B and SLC26A4 heterozygous variations by Sanger sequencing.ConclusionsPresence of multiple genetic homozygous variants of SLC26A4 and VPS13B, it is difficult to make an early diagnosis due to early atypical symptoms. Final diagnosis depends on whole exome sequencing which plays an important role in early diagnosis of intractable neonatal cases.