# NM_153240.5(NPHP3):c.434_437del (p.Glu145fs)

https://sugi.bio/variant/nphp3-p-glu145fs

## Summary

**NPHP3 p.Glu145fs (c.434_437del)** is classified **Pathogenic** in NPHP3 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-09-11). Ultra-rare (popmax 0.0134%, amr); Associated with NPHP3-related disorder.

**At a glance:** Pathogenic · review: Multiple submitters · rsID rs763300393 · 6 submitters · 5 linked conditions · ultra-rare (popmax 0.0134%, amr)

## For patients & families {#patients}

This is a change in the NPHP3 gene that is considered disease-causing, submitted by 6 submitters, and is linked to NPHP3-related disorder.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [NPHP3](https://sugi.bio/atlas/gene/NPHP3/) |
| Protein change (HGVS p.) | p.Glu145fs |
| Coding change (HGVS c.) | c.434_437del |
| MANE Select transcript | [NM_153240](https://www.ncbi.nlm.nih.gov/nuccore/NM_153240) |
| dbSNP | [rs763300393](https://www.ncbi.nlm.nih.gov/snp/rs763300393/) |
| Variant type | Microsatellite |
| Location | chr3:132719787-132719790 (GRCh38) |
| ClinVar | [VCV195423](https://www.ncbi.nlm.nih.gov/clinvar/variation/195423/) |

**All HGVS expressions:** `NC_000003.11:g.132438631CTTT[1]`, `NC_000003.12:g.132719787CTTT[1]`, `NG_008130.2:g.7639AAAG[1]`, `NM_153240.5:c.434_437del`, `NR_037804.1:n.534AAAG[1]`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.819, GERP -0.622, phastCons 0.964 — weakly conserved position
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.873, pLI 1.4471e-21. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 2 of 27**, so the transcript is predicted to undergo NMD.
- CADD: **PHRED 34.0**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no microsatellite variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.0134%** (amr) · FAF95 0.00666% · FAF99 0.00485% · 8/59,576 in the highest group · 83/1,601,086 alleles overall — ultra-rare (popmax 0.0134%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.0134% | 7,447 |
| European (non-Finnish) | 0.00614% | 16,277 |
| Remaining individuals (not grpmax-eligible) | 0.00485% | 20,622 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**NPHP3** population constraint: LOEUF 0.873, pLI 1.4471e-21, missense-Z 0.91316. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **nephronophthisis** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 73.59, 9% of residues very-high.

**1 experimental structure(s)** (PDB): [5L7K](https://www.rcsb.org/structure/5L7K).

## What this gene does {#gene-function}

*Describes the biological roles of NPHP3 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*


### Pathways affected {#pathways}

NPHP3 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Trafficking of myristoylated proteins to the cilium](https://reactome.org/content/detail/R-HSA-5624138) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** kidney development, heart looping, atrial septum development, determination of left/right symmetry, lung development, determination of pancreatic left/right asymmetry.

## Clinical significance {#significance}

**Pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-09-11.

**Submitter consensus:** unanimous (6/6 Pathogenic).

**Submission history:** 6 submissions (2014–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Molecular Biology Laboratory, Fundació Puigvert | Pathogenic | criteria provided, single submitter | research | 2020-02-01 |
| Fulgent Genetics, Fulgent Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2021-12-23 |
| Eurofins Ntd Llc (ga) | Pathogenic | criteria provided, single submitter | clinical testing | 2014-09-16 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2025-05-21 |
| GeneDx | Pathogenic | criteria provided, single submitter | clinical testing | 2025-09-11 |
| Blueprint Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2022-08-31 |

## Associated conditions {#conditions}

[NPHP3-related disorder](https://sugi.bio/atlas/disease/nphp3-related-disorder/), [renal-hepatic-pancreatic dysplasia 1](https://sugi.bio/atlas/disease/renal-hepatic-pancreatic-dysplasia-1/), [NPHP3-related Meckel-like syndrome](https://sugi.bio/atlas/disease/nphp3-related-meckel-like-syndrome/), [nephronophthisis 3](https://sugi.bio/atlas/disease/nephronophthisis-3/), [nephronophthisis](https://sugi.bio/atlas/disease/nephronophthisis/).

**Reported phenotype names (ClinVar):** NPHP3-related disorder, not provided, Nephronophthisis 3, Nephronophthisis, NPHP3-related Meckel-like syndrome, Renal-hepatic-pancreatic dysplasia 1, NPHP3-related condition, NPHP3-related disorders, Juvenile Nephronophthisis, GOLDSTON SYNDROME.

## Similar variants {#similar}

Related NPHP3 variant pages (same residue, condition, or type): [NPHP3 p.Ala1135fs](/variant/nphp3-p-ala1135fs), [NPHP3 p.Gly1275del](/variant/nphp3-p-gly1275del), [NPHP3 p.Leu365fs](/variant/nphp3-p-leu365fs), [NPHP3 p.Ser611fs](/variant/nphp3-p-ser611fs), [NPHP3 p.Ser960fs](/variant/nphp3-p-ser960fs), [NPHP3 c.3813-12TC[2]](/variant/nphp3-c-3813-minus-12tc-2), [NPHP3 p.Glu1292del](/variant/nphp3-p-glu1292del), [NPHP3 p.Glu145Gln](/variant/nphp3-p-glu145gln).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 195423). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*