Is BOC p.Val403Ile (c.1207G>A) pathogenic?

BOC p.Val403Ile (c.1207G>A) is classified Uncertain significance in BOC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-11). AlphaMissense: likely benign (0.1384); Ultra-rare (popmax 0.0993%, sas).

How common is BOC p.Val403Ile (c.1207G>A) in the general population?

BOC p.Val403Ile (c.1207G>A) is ultra-rare (popmax 0.0993%, sas) (gnomAD).

What do computational predictors say about BOC p.Val403Ile (c.1207G>A)?

AlphaMissense predicts likely benign (score 0.1384) — an in-silico prediction, not a clinical call.

BOC p.Val403Ile

c.1207G>A · VCV3481465

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1384 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0993%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1384	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -7.12	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 8.6	GERP 2.4, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 37 kb · p 1.8e-07 · regional, not allelic
Overall
CADD	21.7	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 0.0993% South Asian · 90/90,592 alleles

Filtering AF 0.0828% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0765%

Overall 0.00714% 114/1,595,860 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0993%	1,007
Middle Eastern	0.0332%	3,008
Remaining individualsnot grpmax-eligible	0.00974%	10,269
East Asian	0.00225%	44,374
European (non-Finnish)	0.00129%	77,713

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: BOC
Protein: p.Val403Ile
Coding: c.1207G>A
MANE Select: NM_001378074
Type: single nucleotide variant
Location: chr3:113273314 (GRCh38)
Gene constraint: LOEUF 0.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.98 · 3 PDB
Residue 403: the ig-like c2-type 4 domain

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

Similar variants

BOC p.Ala715= Benign ★★ same type
BOC p.Lys884Asn Benign ★★ same type
BOC p.Pro829Arg Benign ★★ same type
BOC p.Pro913Ser Benign ★★ same type
BOC p.Ala226Thr Uncertain significance ★ ⚠ same type
BOC p.Ala424Thr Uncertain significance ★ ⚠ same type
BOC p.Ala470Val Uncertain significance ★ ⚠ same type
BOC p.Ala503Val 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/boc-p-val403ile (accessed [today's date]).

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