Is CTU2 p.Arg490Cys (c.1468C>T) pathogenic?

CTU2 p.Arg490Cys (c.1468C>T) is classified Uncertain significance in CTU2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-02-18). AlphaMissense: likely benign (0.2578); Ultra-rare (popmax 0.0345%, amr).

How common is CTU2 p.Arg490Cys (c.1468C>T) in the general population?

CTU2 p.Arg490Cys (c.1468C>T) is ultra-rare (popmax 0.0345%, amr) (gnomAD).

What do computational predictors say about CTU2 p.Arg490Cys (c.1468C>T)?

AlphaMissense predicts likely benign (score 0.2578) — an in-silico prediction, not a clinical call.

CTU2 p.Arg490Cys

c.1468C>T · rs368079417 · VCV2369716

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2578 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0345%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2578	likely benign
REVEL	0.416	indeterminate
SaProt	LLR -11.32	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 1.2, phastCons 1
Regional constraint	o/e 1.61	unconstrained · MANE · 8,717 bp · p 1.9e-57 · regional, not allelic
Overall
CADD	29.6	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 0.0345% Admixed American · 20/58,046 alleles

Filtering AF 0.0228% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.019%

Overall 0.0119% 189/1,584,152 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0345%	2,902
Middle Eastern	0.0336%	2,976
Remaining individualsnot grpmax-eligible	0.018%	5,567
South Asian	0.0138%	7,242
African / African-American	0.0134%	7,449
East Asian	0.0112%	8,920
European (non-Finnish)	0.0109%	9,169
Ashkenazi Jewishnot grpmax-eligible	0.00361%	27,666
Finnishnot grpmax-eligible	0.00167%	59,844

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: CTU2
Protein: p.Arg490Cys
Coding: c.1468C>T
MANE Select: NM_001012759
dbSNP: rs368079417
Type: single nucleotide variant
Location: chr16:88715096 (GRCh38)
Gene constraint: LOEUF 1.535 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.27

Full CTU2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CTU2 p.Arg490His Uncertain significance ★ ⚠ same residue
CTU2 c.1420-1G>A Likely pathogenic ★★ same type
CTU2 c.282+5G>A Pathogenic ★★ same type
CTU2 p.Gln243Ter Pathogenic/Likely pathogenic ★★ same type
CTU2 p.Thr291= Pathogenic ★★ same type
CTU2 p.Ala176Val Uncertain significance ★★ ⚠ same type
CTU2 p.Ala400Thr Uncertain significance ★★ ⚠ same type
CTU2 p.Arg270Cys 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/ctu2-p-arg490cys (accessed [today's date]).

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