Is APCS p.Ile128Val (c.382A>G) pathogenic?

APCS p.Ile128Val (c.382A>G) is classified Likely benign in APCS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-27). AlphaMissense: likely benign (0.0803); Absent from gnomAD v4.1.

How common is APCS p.Ile128Val (c.382A>G) in the general population?

APCS p.Ile128Val (c.382A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APCS p.Ile128Val (c.382A>G)?

AlphaMissense predicts likely benign (score 0.0803) — an in-silico prediction, not a clinical call.

APCS p.Ile128Val

c.382A>G · VCV3413415

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0803 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0803	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.01	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3	GERP -4
Regional constraint	o/e 1.17	unconstrained · MANE · 783 bp · p 0.0074 · regional, not allelic
Overall
CADD	1.046	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APCS
Protein: p.Ile128Val
Coding: c.382A>G
MANE Select: NM_001639
Type: single nucleotide variant
Location: chr1:159588418 (GRCh38)
Gene constraint: LOEUF 1.826 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 94.48 · 13 PDB
Residue 128: a β-strand; the pentraxin (ptx) domain

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

Similar variants

APCS p.Ala146Thr Uncertain significance ★ ⚠ same type
APCS p.Ala58Val Uncertain significance ★ ⚠ same type
APCS p.Arg64His Uncertain significance ★ ⚠ same type
APCS p.Arg86Gly Uncertain significance ★ ⚠ same type
APCS p.Asp203His Uncertain significance ★ ⚠ same type
APCS p.Gln74Glu Uncertain significance ★ ⚠ same type
APCS p.Glu118Lys Uncertain significance ★ same type
APCS p.Ile113Asn Uncertain significance ★ ⚠ 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/apcs-p-ile128val (accessed [today's date]).

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