Is ATAD5 p.Pro887Ala (c.2659C>G) pathogenic?

ATAD5 p.Pro887Ala (c.2659C>G) is classified Uncertain significance in ATAD5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-31). AlphaMissense: likely benign (0.0891); Absent from gnomAD v4.1.

How common is ATAD5 p.Pro887Ala (c.2659C>G) in the general population?

ATAD5 p.Pro887Ala (c.2659C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ATAD5 p.Pro887Ala (c.2659C>G)?

AlphaMissense predicts likely benign (score 0.0891) — an in-silico prediction, not a clinical call.

ATAD5 p.Pro887Ala

c.2659C>G · rs1368973061 · VCV2531826

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0891 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.0891	likely benign
REVEL	0.315	indeterminate
SaProt	LLR -6.57	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.37, phastCons 1
Regional constraint	o/e 0.85	unconstrained · MANE · 33 kb · p 0.0003 · regional, not allelic
Overall
CADD	17.22	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

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: ATAD5
Protein: p.Pro887Ala
Coding: c.2659C>G
MANE Select: NM_024857
dbSNP: rs1368973061
Type: single nucleotide variant
Location: chr17:30856978 (GRCh38)
Gene constraint: LOEUF 0.417 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 46.76 · 4 PDB
Residue 887: an α-helix

Full ATAD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ATAD5 c.4013-8G>A Benign ★★ same type
ATAD5 p.Asp826= Likely benign ★★ same type
ATAD5 p.Ala1326Thr Uncertain significance ★ ⚠ same type
ATAD5 p.Ala1459Thr Uncertain significance ★ ⚠ same type
ATAD5 p.Ala1539Pro Uncertain significance ★ ⚠ same type
ATAD5 p.Ala1711Val Uncertain significance ★ ⚠ same type
ATAD5 p.Ala326Val Uncertain significance ★ ⚠ same type
ATAD5 p.Ala414Thr 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/atad5-p-pro887ala (accessed [today's date]).

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