Is ACD p.Cys69Ser (c.206G>C) pathogenic?

ACD p.Cys69Ser (c.206G>C) is classified Uncertain significance in ACD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-06-11). AlphaMissense: likely pathogenic (0.8856); Absent from gnomAD v4.1; Associated with dyskeratosis congenita, autosomal dominant 6.

What condition is associated with ACD p.Cys69Ser (c.206G>C)?

ACD p.Cys69Ser (c.206G>C) is associated with dyskeratosis congenita, autosomal dominant 6 (ClinVar).

How common is ACD p.Cys69Ser (c.206G>C) in the general population?

ACD p.Cys69Ser (c.206G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACD p.Cys69Ser (c.206G>C)?

AlphaMissense predicts likely pathogenic (score 0.8856) — an in-silico prediction, not a clinical call.

ACD p.Cys69Ser

c.206G>C · rs748312961 · VCV1413267

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8856 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

dyskeratosis congenita, autosomal dominant 6

Computational evidence

Protein change
AlphaMissense	0.8856	likely pathogenic · top 5% in ACD
REVEL	0.282	benign-leaning
SaProt	LLR -9.12	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 5.9	GERP 1.4, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 2,611 bp · p 0.011 · regional, not allelic
Overall
CADD	28.0	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

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: ACD
Protein: p.Cys69Ser
Coding: c.206G>C
MANE Select: NM_001082486
dbSNP: rs748312961
Type: single nucleotide variant
Location: chr16:67659939 (GRCh38)
Gene constraint: LOEUF 0.921 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.09 · 28 PDB
Residue 69: a β-strand

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

Disease context

dyskeratosis congenita, autosomal dominant 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACD p.Cys69= Likely benign ★★ same residue
ACD p.Cys69Trp Uncertain significance ★ ⚠ same residue
ACD p.Trp69Arg Uncertain significance ★ same residue
ACD c.645+2T>C Uncertain significance ★★ same condition
ACD c.99+5G>A Uncertain significance ★★ same condition
ACD c.-20C>T Uncertain significance ★★ same condition
ACD c.-24C>T Uncertain significance ★★ same condition
ACD c.-26T>G 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/acd-p-cys69ser (accessed [today's date]).

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