| | | Single nucleotide variant (3 prime UTR variant) | Kidney disorder | |
| | NPHP3, NPHP3-ACAD11 (F1324S) | Single nucleotide variant (non-coding transcript variant +1 more) | Nephronophthisis +3 more | GConflicting classifications of pathogenicity |
| | NPHP3, NPHP3-ACAD11 (R1305C) | Single nucleotide variant (non-coding transcript variant +1 more) | not specified +6 more | |
| | | Single nucleotide variant (non-coding transcript variant +1 more) | NPHP3-related Meckel-like syndrome +6 more | |
| | | Single nucleotide variant (intron variant) | Kidney disorder +5 more | GConflicting classifications of pathogenicity |
| | NPHP3, NPHP3-ACAD11 (R1167H) | Single nucleotide variant (non-coding transcript variant +1 more) | Nephronophthisis +3 more | GConflicting classifications of pathogenicity |
| | NPHP3, NPHP3-ACAD11 (Y1104C) | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder +5 more | |
| | | Single nucleotide variant (non-coding transcript variant +1 more) | NPHP3-related Meckel-like syndrome +6 more | |
| | | Single nucleotide variant (non-coding transcript variant +1 more) | NPHP3-related Meckel-like syndrome +6 more | GConflicting classifications of pathogenicity |
| | NPHP3, NPHP3-ACAD11 (F890L) | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder | |
| | | Single nucleotide variant (intron variant) | Nephronophthisis +5 more | |
| | NPHP3, NPHP3-ACAD11 (N711S) | Single nucleotide variant (non-coding transcript variant +1 more) | Atypical hemolytic-uremic syndrome +4 more | GConflicting classifications of pathogenicity |
| | NPHP3-ACAD11, NPHP3 (I681R) | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder | |
| | NPHP3-ACAD11, NPHP3 (N653S) | Single nucleotide variant (missense variant) | Kidney disorder | |
| | | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder +5 more | |
| | NPHP3-ACAD11, NPHP3 (G238A) | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder | |
| | | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder +5 more | |
| | NPHP3, NPHP3-ACAD11 (A150V) | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder +5 more | |
| | LOC129937586, NPHP3 +2 more (A52T) | Single nucleotide variant (non-coding transcript variant +1 more) | Nephronophthisis 3 +6 more | GConflicting classifications of pathogenicity |
| | LOC129937586, NPHP3 +2 more | Single nucleotide variant (non-coding transcript variant +1 more) | not provided +6 more | GConflicting classifications of pathogenicity |
| | NPHP3-ACAD11, NPHP3-AS1 +2 more | Single nucleotide variant (non-coding transcript variant +1 more) | Kidney disorder +5 more | |