Is ATP5PD p.Ala110Val (c.329C>T) pathogenic?

ATP5PD p.Ala110Val (c.329C>T) is classified Uncertain significance in ATP5PD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-15). AlphaMissense: likely benign (0.1165); Very rare (popmax 0.0011%, sas).

How common is ATP5PD p.Ala110Val (c.329C>T) in the general population?

ATP5PD p.Ala110Val (c.329C>T) is very rare (popmax 0.0011%, sas) (gnomAD).

What do computational predictors say about ATP5PD p.Ala110Val (c.329C>T)?

AlphaMissense predicts likely benign (score 0.1165) — an in-silico prediction, not a clinical call.

ATP5PD p.Ala110Val

c.329C>T · rs1450085053 · VCV2602340

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1165 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1165	likely benign
REVEL	0.029	moderately benign-leaning
SaProt	LLR -8.94	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.25	loss · gain 0.04 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.048	GERP -1.7
Regional constraint	o/e 0.88	unconstrained · MANE · 3,715 bp · p 0.093 · regional, not allelic
Overall
CADD	14.52	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,076 alleles

Overall 6.84e-05% 1/1,461,864 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ATP5PD
Protein: p.Ala110Val
Coding: c.329C>T
MANE Select: NM_006356
dbSNP: rs1450085053
Type: single nucleotide variant
Location: chr17:75039234 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.11 · 14 PDB
Residue 110: an α-helix

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.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
ATP5PD p.Ile19Val 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-ala110val (accessed [today's date]).

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