Is RUNX1 p.Pro333= (c.999G>T) pathogenic?

RUNX1 p.Pro333= (c.999G>T) is classified Likely benign in RUNX1 (ClinVar, Expert panel, 2 submitters; last evaluated 2024-06-24). Very rare (popmax 0.00017%, nfe); Associated with hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1.

How common is RUNX1 p.Pro333= (c.999G>T) in the general population?

RUNX1 p.Pro333= (c.999G>T) is very rare (popmax 0.00017%, nfe) (gnomAD).

RUNX1 p.Pro333=

Q: What condition is associated with RUNX1 p.Pro333= (c.999G>T)?

RUNX1 p.Pro333= (c.999G>T) is associated with hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 (ClinVar).

Q: How is Familial platelet disorder with associated myeloid malignancy inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.999G>T · rs956885198 · VCV1628628

Likely benign Expert panel

Classification

Likely benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Conditions

hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1

ClinGen expert panel — Myeloid Malignancy VCEP

Likely Benign for hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1. Applied ACMG criteria (verbatim):

PM2_Supporting BP7 BP4

Curation rationale (ClinGen, verbatim)

This synonymous variant has a SpliceAI Δ score of 0.00 (BP4). Evolutionary conservation prediction algorithms predict the site as not being conserved (PhyloP score -0.008 (< 2)) (BP7). This variant is completely absent from all population databases with at least 20x coverage for RUNX1 (PM2_supporting). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, BP7, PM2_supporting.

ClinGen Evidence Repository → · reported verbatim, not re-tallied by Sugi Variant.

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.3	GERP -5.1
Overall
CADD	2.074	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,174,786 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000125% 2/1,602,266 alleles · very rare exomes 2/1,450,256 · genomes 0/152,010 · joint denominator

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: RUNX1
Protein: p.Pro333=
Coding: c.999G>T
MANE Select: NM_001754
dbSNP: rs956885198
Type: single nucleotide variant
Location: chr21:34792579 (GRCh38)
Gene constraint: LOEUF 0.633 · pLI 0.29 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.76 · 5 PDB
Residue 333: the 'interaction with kat6a' region; the 'interaction with kat6b' region

Full RUNX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary thrombocytopenia and hematological cancer predisposition syndrome associated with RUNX1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial platelet disorder with associated myeloid malignancy (Orphanet):

Inheritance: Autosomal dominant

Similar variants

RUNX1 p.Pro333Arg Uncertain significance ★★★ same residue
RUNX1 p.Pro333Ser Uncertain significance ★★★ ⚠ same residue
RUNX1 p.Pro333Leu Likely benign ★★★ same residue
RUNX1 c.351+1G>A Pathogenic ★★★ same condition
RUNX1 c.351+1G>C Likely pathogenic ★★★ same condition
RUNX1 c.351+2T>A Likely pathogenic ★★★ same condition
RUNX1 c.351+2T>C Likely pathogenic ★★★ same condition
RUNX1 c.352-1G>A 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/runx1-p-pro333 (accessed [today's date]).

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