Is SBF2 p.Thr142= (c.426C>T) pathogenic?

SBF2 p.Thr142= (c.426C>T) is classified Likely benign in SBF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-05). Ultra-rare (popmax 0.085%, amr); Associated with Charcot-Marie-Tooth disease type 4.

What condition is associated with SBF2 p.Thr142= (c.426C>T)?

SBF2 p.Thr142= (c.426C>T) is associated with Charcot-Marie-Tooth disease type 4 (ClinVar).

How common is SBF2 p.Thr142= (c.426C>T) in the general population?

SBF2 p.Thr142= (c.426C>T) is ultra-rare (popmax 0.085%, amr) (gnomAD).

SBF2 p.Thr142=

c.426C>T · rs1368217756 · VCV2139928

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.085%, amr)

Conditions

Charcot-Marie-Tooth disease type 4

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 2.3	GERP -2.3, phastCons 1
Overall
CADD	9.454	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.085% Admixed American · 51/59,984 alleles

Filtering AF 0.0664% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0598%

Overall 0.00341% 55/1,613,046 alleles · ultra-rare exomes 20/1,461,014 · genomes 35/152,032 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.085%	1,176
African / African-American	0.00267%	37,415
European (non-Finnish)	0.00017%	589,644

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.Thr142=
Coding: c.426C>T
MANE Select: NM_030962
dbSNP: rs1368217756
Type: single nucleotide variant
Location: chr11:10029852 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.74
Residue 142: the udenn domain

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

Disease context

Charcot-Marie-Tooth disease type 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SBF2 c.3653-1G>A Likely pathogenic ★★ same condition
SBF2 p.Arg342Ter Pathogenic/Likely pathogenic ★★ same condition
SBF2 p.Arg356Ter Pathogenic ★★ same condition
SBF2 p.Arg487Ter Pathogenic ★★ same condition
SBF2 p.Arg77Ter Pathogenic ★★ same condition
SBF2 c.1601-3T>G Uncertain significance ★★ same condition
SBF2 c.3111-3T>C Uncertain significance ★★ same condition
SBF2 c.3652+5G>A 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-thr142 (accessed [today's date]).

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