Is CRY2 p.Arg487Trp (c.1459C>T) pathogenic?

CRY2 p.Arg487Trp (c.1459C>T) is classified Uncertain significance in CRY2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-16). AlphaMissense: likely benign (0.1235); Very rare (popmax 0.00801%, afr).

How common is CRY2 p.Arg487Trp (c.1459C>T) in the general population?

CRY2 p.Arg487Trp (c.1459C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

What do computational predictors say about CRY2 p.Arg487Trp (c.1459C>T)?

AlphaMissense predicts likely benign (score 0.1235) — an in-silico prediction, not a clinical call.

CRY2 p.Arg487Trp

c.1459C>T · rs372919618 · VCV3077692

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1235 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.1235	likely benign
REVEL	0.372	indeterminate
SaProt	LLR -10.00	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.7	GERP -2.2, phastCons 0.99
Regional constraint	o/e 0.81	unconstrained · MANE · 2,063 bp · p 0.0054 · regional, not allelic
Overall
CADD	29.8	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,928 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00228%

Overall 0.000929% 15/1,614,124 alleles · very rare exomes 10/1,461,892 · genomes 5/152,232 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00801%	12,488
Remaining individualsnot grpmax-eligible	0.0016%	62,486
South Asian	0.0011%	91,094
European (non-Finnish)	0.000593%	168,580

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: CRY2
Protein: p.Arg487Trp
Coding: c.1459C>T
MANE Select: NM_021117
dbSNP: rs372919618
Type: single nucleotide variant
Location: chr11:45870442 (GRCh38)
Gene constraint: LOEUF 0.596 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 85.42
Residue 487: the 'required for inhibition of clock-bmal1-mediated transcription' region

Full CRY2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CRY2 p.Ala12Glu Benign ★★ same type
CRY2 p.Gly269= Benign ★★ same type
CRY2 c.37G>C Uncertain significance ★ same type
CRY2 c.-5C>T Uncertain significance ★ same type
CRY2 p.Ala12Val Uncertain significance ★ ⚠ same type
CRY2 p.Ala14Glu Uncertain significance ★ ⚠ same type
CRY2 p.Ala14Val Uncertain significance ★ ⚠ same type
CRY2 p.Ala16Pro 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/cry2-p-arg487trp (accessed [today's date]).

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