Is SBF2 p.Arg600Trp (c.1798C>T) pathogenic?

SBF2 p.Arg600Trp (c.1798C>T) is classified Uncertain significance in SBF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-12). AlphaMissense: likely pathogenic (0.5689); Ultra-rare (popmax 0.0143%, sas); Associated with Inborn genetic diseases.

What condition is associated with SBF2 p.Arg600Trp (c.1798C>T)?

SBF2 p.Arg600Trp (c.1798C>T) is associated with Inborn genetic diseases (ClinVar).

How common is SBF2 p.Arg600Trp (c.1798C>T) in the general population?

SBF2 p.Arg600Trp (c.1798C>T) is ultra-rare (popmax 0.0143%, sas) (gnomAD).

What do computational predictors say about SBF2 p.Arg600Trp (c.1798C>T)?

AlphaMissense predicts likely pathogenic (score 0.5689) — an in-silico prediction, not a clinical call.

SBF2 p.Arg600Trp

c.1798C>T · VCV3950365

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5689 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0143%, sas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.5689	likely pathogenic
REVEL	0.544	indeterminate
SaProt	LLR -10.73	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.5	GERP 0.5, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 514 kb · p 7.7e-06 · regional, not allelic
Overall
CADD	25.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0143% South Asian · 13/91,082 alleles

Filtering AF 0.00844% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00661%

Overall 0.00136% 22/1,613,916 alleles · ultra-rare exomes 22/1,461,730 · genomes 0/152,186 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0143%	7,006
East Asian	0.00446%	22,431
Admixed American	0.00167%	60,002
African / African-American	0.00133%	75,000
European (non-Finnish)	0.000424%	235,983

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.Arg600Trp
Coding: c.1798C>T
MANE Select: NM_030962
Type: single nucleotide variant
Location: chr11:9962019 (GRCh38)
Gene constraint: LOEUF 0.591 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.74

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.Arg600Gln Uncertain significance ★★ ⚠ same residue
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

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-arg600trp (accessed [today's date]).

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