Is CCT3 p.Met490Val (c.1468A>G) pathogenic?

CCT3 p.Met490Val (c.1468A>G) is classified Uncertain significance in CCT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-15). AlphaMissense: likely benign (0.256); Very rare (popmax 0.00167%, amr).

How common is CCT3 p.Met490Val (c.1468A>G) in the general population?

CCT3 p.Met490Val (c.1468A>G) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about CCT3 p.Met490Val (c.1468A>G)?

AlphaMissense predicts likely benign (score 0.256) — an in-silico prediction, not a clinical call.

CCT3 p.Met490Val

c.1468A>G · VCV4829969

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.256 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.256	likely benign
REVEL	0.837	moderately pathogenic-leaning
SaProt	LLR -4.44	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 1.9, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 29 kb · p 0.0019 · regional, not allelic
Overall
CADD	24.1	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 0.00167% Admixed American · 1/59,998 alleles

Filtering AF 0.000542% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000428%

Overall 0.000805% 13/1,613,994 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,998
European (non-Finnish)	0.00102%	98,329

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: CCT3
Protein: p.Met490Val
Coding: c.1468A>G
MANE Select: NM_005998
Type: single nucleotide variant
Location: chr1:156310623 (GRCh38)
Gene constraint: LOEUF 0.282 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.23 · 72 PDB
Residue 490: an α-helix

Full CCT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCT3 p.Ala307Thr Uncertain significance ★ ⚠ same type
CCT3 p.Ala421Gly Uncertain significance ★ ⚠ same type
CCT3 p.Ala457Ser Uncertain significance ★ ⚠ same type
CCT3 p.Arg127Cys Uncertain significance ★ ⚠ same type
CCT3 p.Arg167Gln Uncertain significance ★ ⚠ same type
CCT3 p.Arg16Cys Uncertain significance ★ ⚠ same type
CCT3 p.Arg230Gln Uncertain significance ★ ⚠ same type
CCT3 p.Arg230Trp 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/cct3-p-met490val (accessed [today's date]).

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