Is ALDOC p.Pro6Leu (c.17C>T) pathogenic?

ALDOC p.Pro6Leu (c.17C>T) is classified Uncertain significance in ALDOC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-10). AlphaMissense: likely benign (0.184); Ultra-rare (popmax 0.0226%, afr).

How common is ALDOC p.Pro6Leu (c.17C>T) in the general population?

ALDOC p.Pro6Leu (c.17C>T) is ultra-rare (popmax 0.0226%, afr) (gnomAD).

What do computational predictors say about ALDOC p.Pro6Leu (c.17C>T)?

AlphaMissense predicts likely benign (score 0.184) — an in-silico prediction, not a clinical call.

ALDOC p.Pro6Leu

c.17C>T · VCV3283862

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.184 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0226%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.184	likely benign
REVEL	0.467	indeterminate
SaProt	LLR -10.78	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.9, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 2,003 bp · p 1.9e-08 · regional, not allelic
Overall
CADD	25.8	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 0.0226% African / African-American · 17/75,068 alleles

Filtering AF 0.0144% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0118%

Overall 0.00149% 24/1,614,084 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0226%	4,416
Admixed American	0.0117%	8,575

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: ALDOC
Protein: p.Pro6Leu
Coding: c.17C>T
MANE Select: NM_005165
Type: single nucleotide variant
Location: chr17:28575516 (GRCh38)
Gene constraint: LOEUF 0.785 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.43 · 1 PDB

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

Similar variants

ALDOC p.Ala136Asp Uncertain significance ★ ⚠ same type
ALDOC p.Ala297Thr Uncertain significance ★ ⚠ same type
ALDOC p.Ala297Val Uncertain significance ★ ⚠ same type
ALDOC p.Ala32Ser Uncertain significance ★ ⚠ same type
ALDOC p.Arg134Cys Uncertain significance ★ ⚠ same type
ALDOC p.Arg134His Uncertain significance ★ ⚠ same type
ALDOC p.Arg149Cys Uncertain significance ★ ⚠ same type
ALDOC p.Arg157Cys 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/aldoc-p-pro6leu (accessed [today's date]).

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