Is BRAF p.Pro420Arg (c.1259C>G) pathogenic?

BRAF p.Pro420Arg (c.1259C>G) is classified Uncertain significance in BRAF (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-14). AlphaMissense: ambiguous (0.4769); Absent from gnomAD v4.1; Associated with RASopathy.

What condition is associated with BRAF p.Pro420Arg (c.1259C>G)?

BRAF p.Pro420Arg (c.1259C>G) is associated with RASopathy (ClinVar).

How common is BRAF p.Pro420Arg (c.1259C>G) in the general population?

BRAF p.Pro420Arg (c.1259C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRAF p.Pro420Arg (c.1259C>G)?

AlphaMissense predicts ambiguous (score 0.4769) — an in-silico prediction, not a clinical call.

BRAF p.Pro420Arg

c.1259C>G · rs2536185713 · VCV2752496

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4769 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

RASopathy

Computational evidence

Protein change
AlphaMissense	0.4769	ambiguous
REVEL	0.515	indeterminate
SaProt	LLR -8.79	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 3.5, phastCons 1
Overall
CADD	32.0	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: BRAF
Protein: p.Pro420Arg
Coding: c.1259C>G
MANE Select: NM_004333
dbSNP: rs2536185713
Type: single nucleotide variant
Location: chr7:140783076 (GRCh38)
Gene constraint: LOEUF 0.237 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 67.87 · 135 PDB
Residue 420: the 'disordered' region

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

Disease context

RASopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BRAF p.Pro420= Likely benign ★★ same residue
BRAF p.Pro420Ser Uncertain significance ★ ⚠ same residue
BRAF p.Ala246Pro Pathogenic ★★★ same condition
BRAF p.Asn581Asp Pathogenic ★★★ same condition
BRAF p.Asp594Val Pathogenic ★★★ same condition
BRAF p.Cys532Tyr Likely pathogenic ★★★ same condition
BRAF p.Gln257Arg Pathogenic ★★★ same condition
BRAF p.Gly265Arg Likely pathogenic ★★★ 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/braf-p-pro420arg (accessed [today's date]).

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