Is APC2 p.Ser1360Pro (c.4078T>C) pathogenic?

APC2 p.Ser1360Pro (c.4078T>C) is classified Uncertain significance in APC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-08). AlphaMissense: likely benign (0.1339); Very rare (popmax 0.00291%, afr); Associated with Inborn genetic diseases.

What condition is associated with APC2 p.Ser1360Pro (c.4078T>C)?

APC2 p.Ser1360Pro (c.4078T>C) is associated with Inborn genetic diseases (ClinVar).

How common is APC2 p.Ser1360Pro (c.4078T>C) in the general population?

APC2 p.Ser1360Pro (c.4078T>C) is very rare (popmax 0.00291%, afr) (gnomAD).

What do computational predictors say about APC2 p.Ser1360Pro (c.4078T>C)?

AlphaMissense predicts likely benign (score 0.1339) — an in-silico prediction, not a clinical call.

APC2 p.Ser1360Pro

c.4078T>C · rs778482906 · VCV2535458

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1339 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00291%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1339	likely benign
REVEL	0.356	indeterminate
SaProt	LLR -6.00	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.3	GERP 1.5, phastCons 1
Overall
CADD	19.26	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00291% African / African-American · 2/68,632 alleles

Filtering AF 0.000484% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000181%

Overall 0.000606% 9/1,485,336 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00291%	34,316
European (non-Finnish)	0.000623%	160,526

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.Ser1360Pro
Coding: c.4078T>C
MANE Select: NM_005883
dbSNP: rs778482906
Type: single nucleotide variant
Location: chr19:1467379 (GRCh38)
Gene constraint: LOEUF 0.961 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 48.87
Residue 1360: the '5 x 20 aa approximate repeat of f-x-v-e-x-t-p-x-c-f-s-r-x-s-s-l-s-s-l-s' region; the 'interaction with ctnnb1' region; a UniProt-annotated variant site (in cdcbm10)

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.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
APC2 p.Ala1492Glu 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-ser1360pro (accessed [today's date]).

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