Is SBF2 p.Arg1679= (c.5037C>T) pathogenic?

SBF2 p.Arg1679= (c.5037C>T) is classified Conflicting classifications of pathogenicity in SBF2 (ClinVar, Conflicting submitters, 10 submitters; last evaluated 2025-12-20). Rare (popmax 0.276%, eas); Associated with Inborn genetic diseases.

What condition is associated with SBF2 p.Arg1679= (c.5037C>T)?

SBF2 p.Arg1679= (c.5037C>T) is associated with Inborn genetic diseases, Charcot-Marie-Tooth disease type 4B2, Charcot-Marie-Tooth disease (ClinVar).

How common is SBF2 p.Arg1679= (c.5037C>T) in the general population?

SBF2 p.Arg1679= (c.5037C>T) is rare (popmax 0.276%, eas) (gnomAD).

SBF2 p.Arg1679=

c.5037C>T · rs200784979 · VCV383688

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

rare (popmax 0.276%, eas)

Conditions

Inborn genetic diseases

⚠ 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 -1.5	GERP -3.8
Overall
CADD	1.39	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.276% East Asian · 124/44,880 alleles

Filtering AF 0.237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.222%

Overall 0.0499% 805/1,613,646 alleles · rare exomes 738/1,461,386 · genomes 67/152,260 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.276%	362
Finnishnot grpmax-eligible	0.197%	508
European (non-Finnish)	0.0447%	2,238
Remaining individualsnot grpmax-eligible	0.0272%	3,675
Admixed American	0.0133%	7,503
African / African-American	0.004%	25,003

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.Arg1679=
Coding: c.5037C>T
MANE Select: NM_030962
dbSNP: rs200784979
Type: single nucleotide variant
Location: chr11:9787634 (GRCh38)

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

Also linked: Charcot-Marie-Tooth disease type 4B2 Charcot-Marie-Tooth disease Charcot-Marie-Tooth disease type 4

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-arg1679 (accessed [today's date]).

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