Is SBF2 p.Pro269= (c.807A>T) pathogenic?

SBF2 p.Pro269= (c.807A>T) is classified Likely benign in SBF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-07-11). Very rare (popmax 0.00167%, amr); Associated with Inborn genetic diseases.

What condition is associated with SBF2 p.Pro269= (c.807A>T)?

SBF2 p.Pro269= (c.807A>T) is associated with Inborn genetic diseases (ClinVar).

How common is SBF2 p.Pro269= (c.807A>T) in the general population?

SBF2 p.Pro269= (c.807A>T) is very rare (popmax 0.00167%, amr) (gnomAD).

SBF2 p.Pro269=

c.807A>T · rs1057521879 · VCV384154

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.55	GERP -3.3, phastCons 1
Overall
CADD	8.409	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/60,024 alleles

Overall 6.22e-05% 1/1,607,972 alleles · very rare exomes 1/1,455,642 · genomes 0/152,330 · 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: SBF2
Protein: p.Pro269=
Coding: c.807A>T
MANE Select: NM_030962
dbSNP: rs1057521879
Type: single nucleotide variant
Location: chr11:10000968 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.74
Residue 269: the cdenn domain

Full SBF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SBF2 p.Arg77Ter Pathogenic ★★ same condition
SBF2 c.1601-3T>G Uncertain significance ★★ same condition
SBF2 c.4258-4C>G Uncertain significance ★★ same condition
SBF2 p.Ala117Gly Uncertain significance ★★ ⚠ same condition
SBF2 p.Arg1173His Uncertain significance ★★ ⚠ same condition
SBF2 p.Arg1176Gln Uncertain significance ★★ ⚠ same condition
SBF2 p.Arg1312Gln Uncertain significance ★★ ⚠ same condition
SBF2 p.Arg1347Trp Uncertain significance ★★ ⚠ 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/sbf2-p-pro269 (accessed [today's date]).

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