Is SBF2 p.Val1158= (c.3474C>T) pathogenic?

SBF2 p.Val1158= (c.3474C>T) is classified Likely benign in SBF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-27). Very rare (popmax 0.00549%, sas); Associated with Charcot-Marie-Tooth disease type 4.

What condition is associated with SBF2 p.Val1158= (c.3474C>T)?

SBF2 p.Val1158= (c.3474C>T) is associated with Charcot-Marie-Tooth disease type 4 (ClinVar).

How common is SBF2 p.Val1158= (c.3474C>T) in the general population?

SBF2 p.Val1158= (c.3474C>T) is very rare (popmax 0.00549%, sas) (gnomAD).

SBF2 p.Val1158=

c.3474C>T · rs376295625 · VCV696791

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Conditions

Charcot-Marie-Tooth disease type 4

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.004	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1	GERP -5.8
Overall
CADD	6.655	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00549% South Asian · 5/91,050 alleles

Filtering AF 0.00315% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00353% 57/1,613,400 alleles · very rare exomes 55/1,461,388 · genomes 2/152,012 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,210
European (non-Finnish)	0.00407%	24,575
East Asian	0.00223%	44,878
Remaining individualsnot grpmax-eligible	0.0016%	62,476
Finnishnot grpmax-eligible	0.00156%	64,010
African / African-American	0.00134%	74,824

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.Val1158=
Coding: c.3474C>T
MANE Select: NM_030962
dbSNP: rs376295625
Type: single nucleotide variant
Location: chr11:9832402 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.74
Residue 1158: the myotubularin phosphatase 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-val1158 (accessed [today's date]).

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