Is ADPRS p.Ala9Val (c.26C>T) pathogenic?

ADPRS p.Ala9Val (c.26C>T) is classified Uncertain significance in ADPRS (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-19). AlphaMissense: likely benign (0.2038); Very rare (popmax 0.00427%, afr); Associated with Inborn genetic diseases.

What condition is associated with ADPRS p.Ala9Val (c.26C>T)?

ADPRS p.Ala9Val (c.26C>T) is associated with Inborn genetic diseases (ClinVar).

How common is ADPRS p.Ala9Val (c.26C>T) in the general population?

ADPRS p.Ala9Val (c.26C>T) is very rare (popmax 0.00427%, afr) (gnomAD).

What do computational predictors say about ADPRS p.Ala9Val (c.26C>T)?

AlphaMissense predicts likely benign (score 0.2038) — an in-silico prediction, not a clinical call.

ADPRS p.Ala9Val

c.26C>T · rs777166159 · VCV2613243

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2038 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00427%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2038	likely benign
REVEL	0.073	moderately benign-leaning
SaProt	LLR -9.20	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.92	GERP 1.5, phastCons 0.006
Regional constraint	o/e 1.00	unconstrained · MANE · 4,478 bp · p 0.95 · regional, not allelic
Overall
CADD	19.08	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 0.00427% African / African-American · 3/70,294 alleles

Filtering AF 0.00113% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000614%

Overall 0.00059% 9/1,525,758 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00427%	23,431
European (non-Finnish)	0.000526%	190,235

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: ADPRS
Protein: p.Ala9Val
Coding: c.26C>T
MANE Select: NM_017825
dbSNP: rs777166159
Type: single nucleotide variant
Location: chr1:36088930 (GRCh38)
Gene constraint: LOEUF 1.155 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.70 · 14 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ADPRS p.Ala94Asp Uncertain significance ★★ ⚠ same condition
ADPRS p.Ala5Val Likely benign ★★ ⚠ same condition
ADPRS c.517-4C>G Uncertain significance ★ same condition
ADPRS p.Ala101Thr Uncertain significance ★ ⚠ same condition
ADPRS p.Ala14Pro Uncertain significance ★ ⚠ same condition
ADPRS p.Ala16Gly Uncertain significance ★ ⚠ same condition
ADPRS p.Ala191Thr Uncertain significance ★ ⚠ same condition
ADPRS p.Ala195Ser 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/adprs-p-ala9val (accessed [today's date]).

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