Is CBR1 p.Arg159Cys (c.475C>T) pathogenic?

CBR1 p.Arg159Cys (c.475C>T) is classified Uncertain significance in CBR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-26). AlphaMissense: likely benign (0.1213); Very rare (popmax 0.00862%, amr).

How common is CBR1 p.Arg159Cys (c.475C>T) in the general population?

CBR1 p.Arg159Cys (c.475C>T) is very rare (popmax 0.00862%, amr) (gnomAD).

What do computational predictors say about CBR1 p.Arg159Cys (c.475C>T)?

AlphaMissense predicts likely benign (score 0.1213) — an in-silico prediction, not a clinical call.

CBR1 p.Arg159Cys

c.475C>T · rs773560089 · VCV2211224

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1213 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00862%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1213	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -8.04	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 -4.9	GERP -0.23
Regional constraint	o/e 0.98	unconstrained · MANE · 2,763 bp · p 0.69 · regional, not allelic
Overall
CADD	20.6	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 0.00862% Admixed American · 5/57,990 alleles

Filtering AF 0.00335% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00287%

Overall 0.00355% 57/1,605,350 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00862%	11,598
European (non-Finnish)	0.00416%	24,013
Remaining individualsnot grpmax-eligible	0.00323%	30,989
Finnishnot grpmax-eligible	0.00157%	63,844

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: CBR1
Protein: p.Arg159Cys
Coding: c.475C>T
MANE Select: NM_001757
dbSNP: rs773560089
Type: single nucleotide variant
Location: chr21:36072523 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.88 · 6 PDB
Residue 159: an α-helix

Full CBR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CBR1 p.Arg159His Uncertain significance ★ ⚠ same residue
CBR1 p.Thr197= Benign ★★ same type
CBR1 p.Ala209Thr Uncertain significance ★ ⚠ same type
CBR1 p.Ala255Val Uncertain significance ★ ⚠ same type
CBR1 p.Ala52Val Uncertain significance ★ ⚠ same type
CBR1 p.Arg119Gln Uncertain significance ★ ⚠ same type
CBR1 p.Arg232Lys Uncertain significance ★ ⚠ same type
CBR1 p.Arg42Gly 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/cbr1-p-arg159cys (accessed [today's date]).

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