Is APC2 p.Ser108Arg (c.322A>C) pathogenic?

APC2 p.Ser108Arg (c.322A>C) is classified Likely benign in APC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-31). AlphaMissense: likely pathogenic (0.7005); Rare (popmax 0.27%, eas); Associated with Inborn genetic diseases.

What condition is associated with APC2 p.Ser108Arg (c.322A>C)?

APC2 p.Ser108Arg (c.322A>C) is associated with Inborn genetic diseases (ClinVar).

How common is APC2 p.Ser108Arg (c.322A>C) in the general population?

APC2 p.Ser108Arg (c.322A>C) is rare (popmax 0.27%, eas) (gnomAD).

What do computational predictors say about APC2 p.Ser108Arg (c.322A>C)?

AlphaMissense predicts likely pathogenic (score 0.7005) — an in-silico prediction, not a clinical call.

APC2 p.Ser108Arg

c.322A>C · rs373808930 · VCV2343572

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7005 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.27%, eas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.7005	likely pathogenic
REVEL	0.368	indeterminate
SaProt	LLR -7.14	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.1	GERP 1.2, phastCons 1
Overall
CADD	24.2	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 0.27% East Asian · 121/44,806 alleles

Filtering AF 0.231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.216%

Overall 0.0101% 163/1,610,744 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.27%	370
Remaining individualsnot grpmax-eligible	0.0529%	1,889
African / African-American	0.00667%	14,999
Admixed American	0.00501%	19,968
European (non-Finnish)	8.48e-05%	1,178,766

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: APC2
Protein: p.Ser108Arg
Coding: c.322A>C
MANE Select: NM_005883
dbSNP: rs373808930
Type: single nucleotide variant
Location: chr19:1453520 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 48.87
Residue 108: the 'disordered' region

Full APC2 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

APC2 p.Ser108Ile Likely benign ★ same residue
APC2 p.Ala1059Glu Uncertain significance ★★ ⚠ same condition
APC2 p.Ala1103Thr Uncertain significance ★★ ⚠ same condition
APC2 p.Ala1116Val Uncertain significance ★★ ⚠ same condition
APC2 p.Ala126Ser Uncertain significance ★★ ⚠ same condition
APC2 p.Ala1311Thr Uncertain significance ★★ ⚠ same condition
APC2 p.Ala1359Val Uncertain significance ★★ ⚠ same condition
APC2 p.Ala1438Thr 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/apc2-p-ser108arg (accessed [today's date]).

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