Is ACD p.Ala57= (c.171G>A) pathogenic?

ACD p.Ala57= (c.171G>A) is classified Likely benign in ACD (ClinVar, Single submitter, 1 submitter; last evaluated 2020-01-07). Very rare (popmax 8.48e-05%, nfe); Associated with Inborn genetic diseases.

What condition is associated with ACD p.Ala57= (c.171G>A)?

ACD p.Ala57= (c.171G>A) is associated with Inborn genetic diseases (ClinVar).

How common is ACD p.Ala57= (c.171G>A) in the general population?

ACD p.Ala57= (c.171G>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

ACD p.Ala57=

c.171G>A · rs1331812977 · VCV1778722

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, 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 -3	GERP -2.7
Overall
CADD	1.619	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,120 alleles

Overall 6.86e-05% 1/1,457,874 alleles · very rare

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.Ala57=
Coding: c.171G>A
MANE Select: NM_001082486
dbSNP: rs1331812977
Type: single nucleotide variant
Location: chr16:67660308 (GRCh38)
Gene constraint: LOEUF 0.921 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 63.09 · 28 PDB
Residue 57: a β-strand

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

Similar variants

ACD p.Thr57Met Uncertain significance ★★ ⚠ same residue
ACD p.Ala57Gly Uncertain significance ★ same residue
ACD p.Ala57Pro Uncertain significance ★ same residue
ACD p.Ala57Ser Uncertain significance ★ same residue
ACD p.Thr57= Likely benign ★ same residue
ACD c.-20C>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-ala57 (accessed [today's date]).

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