Is BOC p.Pro829Arg (c.2486C>G) pathogenic?

BOC p.Pro829Arg (c.2486C>G) is classified Benign in BOC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-01-22). AlphaMissense: likely benign (0.1126); Low-frequency (popmax 1.96%, afr).

How common is BOC p.Pro829Arg (c.2486C>G) in the general population?

BOC p.Pro829Arg (c.2486C>G) is low-frequency (popmax 1.96%, afr) (gnomAD).

What do computational predictors say about BOC p.Pro829Arg (c.2486C>G)?

AlphaMissense predicts likely benign (score 0.1126) — an in-silico prediction, not a clinical call.

BOC p.Pro829Arg

c.2486C>G · rs150200848 · VCV775895

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1126 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.96%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1126	likely benign
REVEL	0.121	moderately benign-leaning
SaProt	LLR -8.45	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 0.85	GERP 0.26
Regional constraint	o/e 0.87	unconstrained · MANE · 37 kb · p 1.8e-07 · regional, not allelic
Overall
CADD	15.44	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM P828R vs ClinVar P829R) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.96% African / African-American · 1,471/75,014 alleles

Filtering AF 1.88% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.84%

Overall 0.106% 1,703/1,613,650 alleles · low-frequency exomes 845/1,461,382 · genomes 858/152,268 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.96%	51
Middle Eastern	0.149%	673
Remaining individualsnot grpmax-eligible	0.142%	702
Admixed American	0.142%	706
South Asian	0.00439%	22,764
European (non-Finnish)	0.00373%	26,810
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606

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.Pro829Arg
Coding: c.2486C>G
MANE Select: NM_001378074
dbSNP: rs150200848
Type: single nucleotide variant
Location: chr3:113283462 (GRCh38)
Gene constraint: LOEUF 0.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.98 · 3 PDB
Residue 828 UniProt numbering: the 'disordered' region

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.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
BOC p.Ala578Thr 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-pro829arg (accessed [today's date]).

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