Is NAA10 p.Gln129Pro (c.386A>C) pathogenic?

NAA10 p.Gln129Pro (c.386A>C) is classified Conflicting classifications of pathogenicity in NAA10 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-10-15). AlphaMissense: likely pathogenic (0.9863); Absent from gnomAD v4.1; Associated with Ogden syndrome.

What condition is associated with NAA10 p.Gln129Pro (c.386A>C)?

NAA10 p.Gln129Pro (c.386A>C) is associated with Ogden syndrome (ClinVar).

How common is NAA10 p.Gln129Pro (c.386A>C) in the general population?

NAA10 p.Gln129Pro (c.386A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NAA10 p.Gln129Pro (c.386A>C)?

AlphaMissense predicts likely pathogenic (score 0.9863) — an in-silico prediction, not a clinical call.

NAA10 p.Gln129Pro

c.386A>C · rs2065169457 · VCV843535

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.9863 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Ogden syndrome

Computational evidence

Protein change
AlphaMissense	0.9863	likely pathogenic
REVEL	0.391	indeterminate
SaProt	LLR -16.47	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.7, phastCons 1
Regional constraint	o/e 0.35	constrained · MANE · 4,115 bp · p 6.6e-13 · regional, not allelic
Overall
CADD	24.9	PHRED · no single calibrated threshold — expert panels disagree

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

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: NAA10
Protein: p.Gln129Pro
Coding: c.386A>C
MANE Select: NM_003491
dbSNP: rs2065169457
Type: single nucleotide variant
Location: chrX:153932071 (GRCh38)
Structure: AlphaFold pLDDT 81.99 · 12 PDB
Residue 129: the n-acetyltransferase domain; a β-strand

Full NAA10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Ogden syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NAA10 p.Gln129Glu Uncertain significance ★ ⚠ same residue
NAA10 p.Ala87Ser Pathogenic/Likely pathogenic ★★ same condition
NAA10 p.Arg116Trp Pathogenic/Likely pathogenic ★★ same condition
NAA10 p.Arg83Cys Pathogenic ★★ same condition
NAA10 p.Glu157Lys Likely pathogenic ★★ ⚠ same condition
NAA10 p.Ile72Thr Likely pathogenic ★★ same condition
NAA10 p.Leu126Val Likely pathogenic ★★ same condition
NAA10 p.Phe128Ile Pathogenic/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/naa10-p-gln129pro (accessed [today's date]).

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