Is CALB2 p.Arg258Cys (c.772C>T) pathogenic?

CALB2 p.Arg258Cys (c.772C>T) is classified Uncertain significance in CALB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-06). AlphaMissense: likely pathogenic (0.66); Very rare (popmax 0.005%, amr).

How common is CALB2 p.Arg258Cys (c.772C>T) in the general population?

CALB2 p.Arg258Cys (c.772C>T) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about CALB2 p.Arg258Cys (c.772C>T)?

AlphaMissense predicts likely pathogenic (score 0.66) — an in-silico prediction, not a clinical call.

CALB2 p.Arg258Cys

c.772C>T · VCV3484332

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.66 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.66	likely pathogenic
REVEL	0.822	moderately pathogenic-leaning
SaProt	LLR -11.33	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP 0.5, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 15 kb · p 0.17 · regional, not allelic
Overall
CADD	24.2	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 0.005% Admixed American · 3/60,002 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00108%

Overall 0.00173% 28/1,613,858 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	20,001
Remaining individualsnot grpmax-eligible	0.0032%	31,242
European (non-Finnish)	0.00195%	51,303

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: CALB2
Protein: p.Arg258Cys
Coding: c.772C>T
MANE Select: NM_001740
Type: single nucleotide variant
Location: chr16:71389821 (GRCh38)
Gene constraint: LOEUF 0.958 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.29
Residue 258: the ef-hand 6 domain

Full CALB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CALB2 p.Ala115Val Uncertain significance ★ ⚠ same type
CALB2 p.Ala129Val Uncertain significance ★ ⚠ same type
CALB2 p.Arg145Gln Uncertain significance ★ ⚠ same type
CALB2 p.Arg145Leu Uncertain significance ★ ⚠ same type
CALB2 p.Arg161Gln Uncertain significance ★ ⚠ same type
CALB2 p.Asn231Ser Uncertain significance ★ ⚠ same type
CALB2 p.Asn236Ser Uncertain significance ★ ⚠ same type
CALB2 p.Asp138His 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/calb2-p-arg258cys (accessed [today's date]).

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