NPHP4 c.1503+1del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,595,710)
Conditions
1
NPHP4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 10 | GERP 1.7, phastCons 1 |
| Non-coding constraint | Z 2.89 | 1 kb window · o/e 0.76 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,595,710). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- NPHP4
- Coding
- c.1503+1del
- MANE Select
- NM_015102
- Type
- Deletion
- Location
- chr1:5909151 (GRCh38)
- Gene constraint
- LOEUF 1.183 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- NPHP4 p.Ala279fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Glu978fs Pathogenic ★★ same condition
- NPHP4 p.Lys424fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Tyr1137fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Val1091fs Pathogenic ★★ same condition
- NPHP4 p.Leu101fs Likely pathogenic ★ same condition
- NPHP4 p.Pro593_Ser594insTer Likely pathogenic ★ same condition
- NPHP4 p.Ser463fs Likely pathogenic ★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nphp4-c-1503-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown