Is ACD p.Pro279= (c.837G>A) pathogenic?

ACD p.Pro279= (c.837G>A) is classified Likely benign in ACD (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-12-03). Ultra-rare (popmax 0.03%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ACD p.Pro279= (c.837G>A)?

ACD p.Pro279= (c.837G>A) is associated with Inborn genetic diseases, dyskeratosis congenita, autosomal dominant 6 (ClinVar).

How common is ACD p.Pro279= (c.837G>A) in the general population?

ACD p.Pro279= (c.837G>A) is ultra-rare (popmax 0.03%, nfe) (gnomAD).

ACD p.Pro279=

c.837G>A · rs201965477 · VCV728419

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.03%, nfe)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.095	GERP -2.8
Overall
CADD	6.452	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.03% European (non-Finnish) · 354/1,179,902 alleles

Filtering AF 0.0274% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0264%

Overall 0.0235% 379/1,613,616 alleles · ultra-rare exomes 355/1,461,350 · genomes 24/152,266 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.03%	3,333
Admixed American	0.0167%	6,002
Remaining individualsnot grpmax-eligible	0.016%	6,248
African / African-American	0.00666%	15,004

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: ACD
Protein: p.Pro279=
Coding: c.837G>A
MANE Select: NM_001082486
dbSNP: rs201965477
Type: single nucleotide variant
Location: chr16:67658355 (GRCh38)
Gene constraint: LOEUF 0.921 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.09 · 28 PDB
Residue 279: the 'disordered' region

Full ACD 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

Also linked: dyskeratosis congenita, autosomal dominant 6

Similar variants

ACD p.Pro279Leu Uncertain significance ★★ ⚠ same residue
ACD p.Pro279Ala 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
ACD c.-29C>A 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-pro279 (accessed [today's date]).

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