Is ACER3 p.Thr17= (c.51G>A) pathogenic?

ACER3 p.Thr17= (c.51G>A) is classified Likely benign in ACER3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-12). Very rare (popmax 0.00366%, nfe).

How common is ACER3 p.Thr17= (c.51G>A) in the general population?

ACER3 p.Thr17= (c.51G>A) is very rare (popmax 0.00366%, nfe) (gnomAD).

ACER3 p.Thr17=

c.51G>A · rs1362201284 · VCV2784611

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00366%, nfe)

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 -0.37	GERP 0.35, phastCons 0.014
Overall
CADD	9.221	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00366% European (non-Finnish) · 42/1,146,456 alleles

Filtering AF 0.00274% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00243%

Overall 0.00308% 43/1,395,878 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00366%	27,297
Remaining individualsnot grpmax-eligible	0.00167%	59,894

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: ACER3
Protein: p.Thr17=
Coding: c.51G>A
MANE Select: NM_018367
dbSNP: rs1362201284
Type: single nucleotide variant
Location: chr11:76861027 (GRCh38)
Gene constraint: LOEUF 0.815 · pLI 0.30 (gnomAD)
Structure: AlphaFold pLDDT 93.23 · 2 PDB

Full ACER3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACER3 p.Ala2Pro Uncertain significance ★★ ⚠ same type
ACER3 p.Ala4Thr Uncertain significance ★★ ⚠ same type
ACER3 p.Arg62Gln Uncertain significance ★★ ⚠ same type
ACER3 p.Gly12Asp Uncertain significance ★★ ⚠ same type
ACER3 p.Ile97Leu Uncertain significance ★★ ⚠ same type
ACER3 p.Val206Ile Uncertain significance ★★ ⚠ same type
ACER3 c.214+19C>G Benign ★★ same type
ACER3 c.320+14A>C Benign ★★ 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/acer3-p-thr17 (accessed [today's date]).

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