Is ATPAF2 p.Pro160= (c.480A>C) pathogenic?

ATPAF2 p.Pro160= (c.480A>C) is classified Uncertain significance in ATPAF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-19). Absent from gnomAD v4.1; Associated with mitochondrial complex V (ATP synthase) deficiency, nuclear type 1.

What condition is associated with ATPAF2 p.Pro160= (c.480A>C)?

ATPAF2 p.Pro160= (c.480A>C) is associated with mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 (ClinVar).

How common is ATPAF2 p.Pro160= (c.480A>C) in the general population?

ATPAF2 p.Pro160= (c.480A>C) is absent from gnomAD v4.1 (gnomAD).

How is Isolated ATP synthase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ATPAF2 p.Pro160=

c.480A>C · rs2044519018 · VCV1027768

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

mitochondrial complex V (ATP synthase) deficiency, nuclear type 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.7	GERP -2.1
Overall
CADD	3.753	PHRED · no single calibrated threshold — expert panels disagree

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: ATPAF2
Protein: p.Pro160=
Coding: c.480A>C
MANE Select: NM_145691
dbSNP: rs2044519018
Type: single nucleotide variant
Location: chr17:18024647 (GRCh38)
Gene constraint: LOEUF 1.1 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.07

Full ATPAF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

mitochondrial complex V (ATP synthase) deficiency, nuclear type 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Isolated ATP synthase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Neonatal

Similar variants

ATPAF2 c.-90C>A Uncertain significance ★★ same condition
ATPAF2 c.*132C>T Uncertain significance ★★ same condition
ATPAF2 p.Ala130Glu Uncertain significance ★★ ⚠ same condition
ATPAF2 p.Ala268Thr Uncertain significance ★★ ⚠ same condition
ATPAF2 p.Arg14Gly Uncertain significance ★★ ⚠ same condition
ATPAF2 p.Arg238His Uncertain significance ★★ ⚠ same condition
ATPAF2 p.Arg38Leu Uncertain significance ★★ ⚠ same condition
ATPAF2 p.Arg3Lys Uncertain significance ★★ ⚠ 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/atpaf2-p-pro160 (accessed [today's date]).

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