Is RAF1 p.Ala142Ser (c.424G>T) pathogenic?

RAF1 p.Ala142Ser (c.424G>T) is classified Uncertain significance in RAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-08-23). AlphaMissense: likely benign (0.286); Absent from gnomAD v4.1.

How common is RAF1 p.Ala142Ser (c.424G>T) in the general population?

RAF1 p.Ala142Ser (c.424G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about RAF1 p.Ala142Ser (c.424G>T)?

AlphaMissense predicts likely benign (score 0.286) — an in-silico prediction, not a clinical call.

RAF1 p.Ala142Ser

c.424G>T · rs1553614748 · VCV505313

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.286 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.286	likely benign
REVEL	0.632	indeterminate
SaProt	LLR -7.43	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.6, phastCons 1
Overall
CADD	29.0	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

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: RAF1
Protein: p.Ala142Ser
Coding: c.424G>T
MANE Select: NM_002880
dbSNP: rs1553614748
Type: single nucleotide variant
Location: chr3:12608923 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.24 · 76 PDB
Residue 142: a β-strand

Full RAF1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RAF1 p.Ala142= Likely benign ★ same residue
RAF1 p.Arg256Ser Likely pathogenic ★★★ ⚠ same type
RAF1 p.Gly361Ala Pathogenic ★★★ ⚠ same type
RAF1 p.Leu613Val Pathogenic ★★★ same type
RAF1 p.Pro261Ser Pathogenic ★★★ ⚠ same type
RAF1 p.Ser257Leu Pathogenic ★★★ ⚠ same type
RAF1 p.Ser257Pro Likely pathogenic ★★★ ⚠ same type
RAF1 p.Ser259Ala Pathogenic ★★★ ⚠ 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/raf1-p-ala142ser (accessed [today's date]).

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