Is NEDD4 p.Pro474Ser (c.1420C>T) pathogenic?

NEDD4 p.Pro474Ser (c.1420C>T) is classified Uncertain significance in NEDD4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-08). AlphaMissense: likely benign (0.2371); Absent from gnomAD v4.1.

How common is NEDD4 p.Pro474Ser (c.1420C>T) in the general population?

NEDD4 p.Pro474Ser (c.1420C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NEDD4 p.Pro474Ser (c.1420C>T)?

AlphaMissense predicts likely benign (score 0.2371) — an in-silico prediction, not a clinical call.

NEDD4 p.Pro474Ser

c.1420C>T · VCV3878660

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2371 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2371	likely benign
REVEL	0.252	benign-leaning
SaProt	LLR -10.82	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 3.9, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 164 kb · p 0.013 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P893S vs ClinVar P474S) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NEDD4
Protein: p.Pro474Ser
Coding: c.1420C>T
MANE Select: NM_006154
Type: single nucleotide variant
Location: chr15:55848814 (GRCh38)
Gene constraint: LOEUF 0.858 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.86 · 15 PDB
Residue 893 UniProt numbering: the ww 4 domain; the 'mediates interaction with tnik' region

Full NEDD4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NEDD4 p.Arg548His Uncertain significance ★★ ⚠ same type
NEDD4 c.1484-6C>T Likely benign ★★ same type
NEDD4 c.291+7901C>A Benign/Likely benign ★★ same type
NEDD4 c.291+7911A>G Benign ★★ same type
NEDD4 c.291+8022G>C Likely benign ★★ same type
NEDD4 c.291+8368T>A Benign/Likely benign ★★ same type
NEDD4 c.291+8666G>A Benign ★★ same type
NEDD4 c.291+8732T>A Benign ★★ same type

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/nedd4-p-pro474ser (accessed [today's date]).

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