Is NPHP3 p.Asp18fs (c.52del) pathogenic?

NPHP3 p.Asp18fs (c.52del) is classified Likely pathogenic in NPHP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-23). No gnomAD frequency available for this variant; Associated with Joubert syndrome and related disorders.

What condition is associated with NPHP3 p.Asp18fs (c.52del)?

NPHP3 p.Asp18fs (c.52del) is associated with Joubert syndrome and related disorders (ClinVar).

How common is NPHP3 p.Asp18fs (c.52del) in the general population?

NPHP3 p.Asp18fs (c.52del) is no gnomAD frequency available for this variant (gnomAD).

NPHP3 p.Asp18fs

c.52del · rs2108008280 · VCV1677181

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Joubert syndrome and related disorders

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.4	GERP 0.14, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: NPHP3
Protein: p.Asp18fs
Coding: c.52del
MANE Select: NM_153240
dbSNP: rs2108008280
Type: Deletion
Location: chr3:132722304 (GRCh38)

Full NPHP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Joubert syndrome and related disorders — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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/nphp3-p-asp18fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown