Is SBF2 p.Phe41Leu (c.123T>A) pathogenic?

SBF2 p.Phe41Leu (c.123T>A) is classified Uncertain significance in SBF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-03). AlphaMissense: likely pathogenic (0.9727); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with SBF2 p.Phe41Leu (c.123T>A)?

SBF2 p.Phe41Leu (c.123T>A) is associated with Inborn genetic diseases (ClinVar).

How common is SBF2 p.Phe41Leu (c.123T>A) in the general population?

SBF2 p.Phe41Leu (c.123T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SBF2 p.Phe41Leu (c.123T>A)?

AlphaMissense predicts likely pathogenic (score 0.9727) — an in-silico prediction, not a clinical call.

SBF2 p.Phe41Leu

c.123T>A · rs2538882249 · VCV3158006

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9727 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9727	likely pathogenic · top 8% in SBF2
REVEL	0.207	benign-leaning
SaProt	LLR -2.80	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP 0.37, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 514 kb · p 7.7e-06 · regional, not allelic
Overall
CADD	21.8	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: SBF2
Protein: p.Phe41Leu
Coding: c.123T>A
MANE Select: NM_030962
dbSNP: rs2538882249
Type: single nucleotide variant
Location: chr11:10193920 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.74
Residue 41: the udenn 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-phe41leu (accessed [today's date]).

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