Is ATP5PD p.Lys63Arg (c.188A>G) pathogenic?

ATP5PD p.Lys63Arg (c.188A>G) is classified Uncertain significance in ATP5PD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-13). AlphaMissense: likely benign (0.1026); Absent from gnomAD v4.1.

How common is ATP5PD p.Lys63Arg (c.188A>G) in the general population?

ATP5PD p.Lys63Arg (c.188A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ATP5PD p.Lys63Arg (c.188A>G)?

AlphaMissense predicts likely benign (score 0.1026) — an in-silico prediction, not a clinical call.

ATP5PD p.Lys63Arg

c.188A>G · VCV3458107

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1026 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1026	likely benign
REVEL	0.444	indeterminate
SaProt	LLR -10.13	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.1	GERP 0.91, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 3,715 bp · p 0.093 · regional, not allelic
Overall
CADD	23.8	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: ATP5PD
Protein: p.Lys63Arg
Coding: c.188A>G
MANE Select: NM_006356
Type: single nucleotide variant
Location: chr17:75042212 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.11 · 14 PDB
Residue 63: a β-strand; a modified residue (n6-acetyllysine)

Full ATP5PD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATP5PD p.Ala102Thr Uncertain significance ★ ⚠ same type
ATP5PD p.Ala110Val Uncertain significance ★ ⚠ same type
ATP5PD p.Ala59Asp Uncertain significance ★ ⚠ same type
ATP5PD p.Asp129Val Uncertain significance ★ ⚠ same type
ATP5PD p.Glu18Asp Uncertain significance ★ ⚠ same type
ATP5PD p.Glu93Lys Uncertain significance ★ ⚠ same type
ATP5PD p.His155Pro Uncertain significance ★ ⚠ same type
ATP5PD p.Ile133Thr Uncertain significance ★ ⚠ 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/atp5pd-p-lys63arg (accessed [today's date]).

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