Is MYB p.Ser403Phe (c.1208C>T) pathogenic?

MYB p.Ser403Phe (c.1208C>T) is classified Uncertain significance in MYB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-07). Absent from gnomAD v4.1.

How common is MYB p.Ser403Phe (c.1208C>T) in the general population?

MYB p.Ser403Phe (c.1208C>T) is absent from gnomAD v4.1 (gnomAD).

MYB p.Ser403Phe

c.1208C>T · VCV4554571

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.077	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 2.6, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 22 kb · p 0.12 · regional, not allelic
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

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: MYB
Protein: p.Ser403Phe
Coding: c.1208C>T
MANE Select: NM_001130173
Type: single nucleotide variant
Location: chr6:135196965 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 59.16
Residue 403: the 'negative regulatory domain' region

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

Similar variants

MYB p.Thr589= Benign/Likely benign ★★ same type
MYB p.Ala278Thr Uncertain significance ★ ⚠ same type
MYB p.Ala470Ser Uncertain significance ★ same type
MYB p.Ala491Asp Uncertain significance ★ same type
MYB p.Ala719Glu Uncertain significance ★ ⚠ same type
MYB p.Arg337Gly Uncertain significance ★ ⚠ same type
MYB p.Arg484Trp Uncertain significance ★ same type
MYB p.Arg4Ser 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/myb-p-ser403phe (accessed [today's date]).

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