Is ADD3 p.Val9Met (c.25G>A) pathogenic?

ADD3 p.Val9Met (c.25G>A) is classified Uncertain significance in ADD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-02). AlphaMissense: likely benign (0.2972); Very rare (popmax 0.00662%, sas).

How common is ADD3 p.Val9Met (c.25G>A) in the general population?

ADD3 p.Val9Met (c.25G>A) is very rare (popmax 0.00662%, sas) (gnomAD).

What do computational predictors say about ADD3 p.Val9Met (c.25G>A)?

AlphaMissense predicts likely benign (score 0.2972) — an in-silico prediction, not a clinical call.

ADD3 p.Val9Met

c.25G>A · rs770809843 · VCV1474374

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2972 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00662%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2972	likely benign
REVEL	0.255	benign-leaning
SaProt	LLR -7.47	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 10	GERP 0.98, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 33 kb · p 0.53 · regional, not allelic
Overall
CADD	27.6	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 0.00662% South Asian · 6/90,648 alleles

Filtering AF 0.00287% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00196%

Overall 0.00103% 15/1,458,820 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00662%	15,108
East Asian	0.00224%	44,644
Admixed American	0.00168%	59,454
Remaining individualsnot grpmax-eligible	0.0016%	62,374
European (non-Finnish)	0.000509%	196,461

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: ADD3
Protein: p.Val9Met
Coding: c.25G>A
MANE Select: NM_016824
dbSNP: rs770809843
Type: single nucleotide variant
Location: chr10:110100678 (GRCh38)
Gene constraint: LOEUF 0.395 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 66.83
Residue 9: the 'disordered' region

Full ADD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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ADD3 p.Arg46Gln Uncertain significance ★★ ⚠ same type
ADD3 p.Arg571His Uncertain significance ★★ ⚠ same type
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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/add3-p-val9met (accessed [today's date]).

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