Is BUD23 p.Arg4Cys (c.10C>T) pathogenic?

BUD23 p.Arg4Cys (c.10C>T) is classified Uncertain significance in BUD23 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-06). AlphaMissense: likely benign (0.1985); Very rare (popmax 0.00534%, afr).

How common is BUD23 p.Arg4Cys (c.10C>T) in the general population?

BUD23 p.Arg4Cys (c.10C>T) is very rare (popmax 0.00534%, afr) (gnomAD).

What do computational predictors say about BUD23 p.Arg4Cys (c.10C>T)?

AlphaMissense predicts likely benign (score 0.1985) — an in-silico prediction, not a clinical call.

BUD23 p.Arg4Cys

c.10C>T · VCV3262336

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1985 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00534%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1985	likely benign
REVEL	0.248	benign-leaning
SaProt	LLR -9.74	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.48	GERP 1.9
Regional constraint	o/e 0.95	unconstrained · MANE · 14 kb · p 0.34 · regional, not allelic
Overall
CADD	17.42	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00534% African / African-American · 4/74,970 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00123%

Overall 0.00205% 33/1,610,874 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00534%	18,742
East Asian	0.00447%	22,379
Finnishnot grpmax-eligible	0.00317%	31,513
European (non-Finnish)	0.00212%	47,159

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: BUD23
Protein: p.Arg4Cys
Coding: c.10C>T
MANE Select: NM_017528
Type: single nucleotide variant
Location: chr7:73683635 (GRCh38)
Gene constraint: LOEUF 0.916 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.37 · 6 PDB

Full BUD23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BUD23 p.Ala195= Benign ★★ same type
BUD23 c.702-107G>A Uncertain significance ★ same type
BUD23 c.702-129G>A Uncertain significance ★ same type
BUD23 c.702-93C>T Uncertain significance ★ same type
BUD23 p.Ala139Ser Uncertain significance ★ ⚠ same type
BUD23 p.Ala23Thr Uncertain significance ★ ⚠ same type
BUD23 p.Ala2Gly Uncertain significance ★ ⚠ same type
BUD23 p.Ala2Val Uncertain significance ★ ⚠ same type

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/bud23-p-arg4cys (accessed [today's date]).

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