Is CIAO2A p.Glu153Lys (c.457G>A) pathogenic?

CIAO2A p.Glu153Lys (c.457G>A) is classified Uncertain significance in CIAO2A (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-13). AlphaMissense: likely pathogenic (0.9308); Very rare (popmax 8.48e-05%, nfe).

How common is CIAO2A p.Glu153Lys (c.457G>A) in the general population?

CIAO2A p.Glu153Lys (c.457G>A) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

What do computational predictors say about CIAO2A p.Glu153Lys (c.457G>A)?

AlphaMissense predicts likely pathogenic (score 0.9308) — an in-silico prediction, not a clinical call.

CIAO2A p.Glu153Lys

c.457G>A · rs970431544 · VCV3144872

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9308 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9308	likely pathogenic
REVEL	0.285	benign-leaning
SaProt	LLR -11.95	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.9, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 21 kb · p 0.97 · regional, not allelic
Overall
CADD	25.4	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 8.48e-05% European (non-Finnish) · 1/1,179,604 alleles

Overall 0.000657% 1/152,194 alleles · very rare

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: CIAO2A
Protein: p.Glu153Lys
Coding: c.457G>A
MANE Select: NM_032231
dbSNP: rs970431544
Type: single nucleotide variant
Location: chr15:64072957 (GRCh38)
Gene constraint: LOEUF 1.054 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 86.90 · 3 PDB
Residue 153: an α-helix; a binding site

Full CIAO2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CIAO2A p.Ala140Val Uncertain significance ★ ⚠ same type
CIAO2A p.Arg149Trp Uncertain significance ★ ⚠ same type
CIAO2A p.Arg14Gly Uncertain significance ★ ⚠ same type
CIAO2A p.Arg48Gln Uncertain significance ★ ⚠ same type
CIAO2A p.Arg48Trp Uncertain significance ★ ⚠ same type
CIAO2A p.Cys155Tyr Uncertain significance ★ ⚠ same type
CIAO2A p.Gln105Glu Uncertain significance ★ ⚠ same type
CIAO2A p.Glu150Lys 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/ciao2a-p-glu153lys (accessed [today's date]).

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