Is CIART p.Ala241Val (c.722C>T) pathogenic?

CIART p.Ala241Val (c.722C>T) is classified Likely benign in CIART (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-28). AlphaMissense: likely benign (0.0587); Very rare (popmax 0.000259%, nfe).

How common is CIART p.Ala241Val (c.722C>T) in the general population?

CIART p.Ala241Val (c.722C>T) is very rare (popmax 0.000259%, nfe) (gnomAD).

What do computational predictors say about CIART p.Ala241Val (c.722C>T)?

AlphaMissense predicts likely benign (score 0.0587) — an in-silico prediction, not a clinical call.

CIART p.Ala241Val

c.722C>T · rs1463018548 · VCV2298475

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0587 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000259%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0587	likely benign
REVEL	0.032	moderately benign-leaning
SaProt	LLR -6.43	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.7	GERP -0.46, phastCons 0.94
Regional constraint	o/e 0.92	unconstrained · MANE · 3,683 bp · p 0.082 · regional, not allelic
Overall
CADD	0.996	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 0.000259% European (non-Finnish) · 3/1,158,496 alleles

Filtering AF 6.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000189% 3/1,590,240 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: CIART
Protein: p.Ala241Val
Coding: c.722C>T
MANE Select: NM_144697
dbSNP: rs1463018548
Type: single nucleotide variant
Location: chr1:150286518 (GRCh38)
Gene constraint: LOEUF 0.606 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 55.07

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

Similar variants

CIART p.Gln162= Benign ★★ same type
CIART p.Ala255Pro Uncertain significance ★ ⚠ same type
CIART p.Ala255Val Uncertain significance ★ ⚠ same type
CIART p.Ala359Pro Uncertain significance ★ ⚠ same type
CIART p.Ala377Val Uncertain significance ★ ⚠ same type
CIART p.Ala380Ser Uncertain significance ★ ⚠ same type
CIART p.Arg160Ser Uncertain significance ★ ⚠ same type
CIART p.Arg367Gln 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/ciart-p-ala241val (accessed [today's date]).

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