Is SBF2 p.Ser1847= (c.5541T>C) pathogenic?

SBF2 p.Ser1847= (c.5541T>C) is classified Likely benign in SBF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-18). Very rare (popmax 0.00223%, eas); Associated with Charcot-Marie-Tooth disease type 4.

What condition is associated with SBF2 p.Ser1847= (c.5541T>C)?

SBF2 p.Ser1847= (c.5541T>C) is associated with Charcot-Marie-Tooth disease type 4 (ClinVar).

How common is SBF2 p.Ser1847= (c.5541T>C) in the general population?

SBF2 p.Ser1847= (c.5541T>C) is very rare (popmax 0.00223%, eas) (gnomAD).

SBF2 p.Ser1847=

c.5541T>C · VCV4728524

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Conditions

Charcot-Marie-Tooth disease type 4

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.086	GERP -2.2, phastCons 0.009
Overall
CADD	9.647	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,880 alleles

Overall 6.2e-05% 1/1,613,776 alleles · very rare exomes 1/1,461,472 · genomes 0/152,304 · 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.Ser1847=
Coding: c.5541T>C
MANE Select: NM_030962
Type: single nucleotide variant
Location: chr11:9780427 (GRCh38)

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

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-ser1847 (accessed [today's date]).

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