Is ADAD2 p.Leu562Pro (c.1685T>C) pathogenic?

ADAD2 p.Leu562Pro (c.1685T>C) is classified Uncertain significance in ADAD2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-06). AlphaMissense: ambiguous (0.4379); Ultra-rare (popmax 0.0122%, amr).

How common is ADAD2 p.Leu562Pro (c.1685T>C) in the general population?

ADAD2 p.Leu562Pro (c.1685T>C) is ultra-rare (popmax 0.0122%, amr) (gnomAD).

What do computational predictors say about ADAD2 p.Leu562Pro (c.1685T>C)?

AlphaMissense predicts ambiguous (score 0.4379) — an in-silico prediction, not a clinical call.

ADAD2 p.Leu562Pro

c.1685T>C · VCV4224377

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4379 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0122%, amr)

Computational evidence

Protein change
AlphaMissense	0.4379	ambiguous
REVEL	0.569	indeterminate
SaProt	LLR -12.41	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.56	GERP -0.51
Regional constraint	o/e 1.38	unconstrained · MANE · 5,740 bp · p 1.6e-26 · regional, not allelic
Overall
CADD	17.55	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

Grpmax group 0.0122% Admixed American · 7/57,486 alleles

Filtering AF 0.00565% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00404%

Overall 0.000484% 7/1,447,370 alleles · ultra-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: ADAD2
Protein: p.Leu562Pro
Coding: c.1685T>C
MANE Select: NM_001145400
Type: single nucleotide variant
Location: chr16:84196907 (GRCh38)
Gene constraint: LOEUF 1.524 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.35
Residue 562: the a to i editase domain; a UniProt-annotated variant site (found in a patient with non-obstructive azoospermia; uncertain significance)

Full ADAD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ADAD2 p.Arg180Gln Likely benign ★★ ⚠ same type
ADAD2 c.419-254A>G Uncertain significance ★ same type
ADAD2 c.419-262T>C Uncertain significance ★ same type
ADAD2 c.419-274C>T Uncertain significance ★ same type
ADAD2 c.419-334G>A Uncertain significance ★ same type
ADAD2 c.419-334G>T Uncertain significance ★ same type
ADAD2 c.419-376A>C Uncertain significance ★ same type
ADAD2 c.419-409G>A 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/adad2-p-leu562pro (accessed [today's date]).

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