Is ART1 p.Pro245Ser (c.733C>T) pathogenic?

ART1 p.Pro245Ser (c.733C>T) is classified Uncertain significance in ART1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-06). AlphaMissense: likely pathogenic (0.6448); Very rare (popmax 0.00975%, nfe).

How common is ART1 p.Pro245Ser (c.733C>T) in the general population?

ART1 p.Pro245Ser (c.733C>T) is very rare (popmax 0.00975%, nfe) (gnomAD).

What do computational predictors say about ART1 p.Pro245Ser (c.733C>T)?

AlphaMissense predicts likely pathogenic (score 0.6448) — an in-silico prediction, not a clinical call.

ART1 p.Pro245Ser

c.733C>T · VCV3432904

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6448 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00975%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.6448	likely pathogenic
REVEL	0.39	indeterminate
SaProt	LLR -12.85	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.7, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 4,972 bp · p 0.0056 · regional, not allelic
Overall
CADD	24.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00975% European (non-Finnish) · 115/1,180,054 alleles

Filtering AF 0.00826% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00774%

Overall 0.00818% 132/1,613,370 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0126%	7,914
European (non-Finnish)grpmax	0.00975%	10,261
Remaining individualsnot grpmax-eligible	0.0096%	10,414
Admixed American	0.00333%	30,001
African / African-American	0.00133%	74,936

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ART1
Protein: p.Pro245Ser
Coding: c.733C>T
MANE Select: NM_004314
Type: single nucleotide variant
Location: chr11:3660252 (GRCh38)
Gene constraint: LOEUF 1.476 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.03
Residue 245: a disulfide bond; the tr mart core domain

Full ART1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ART1 p.Pro245Ala Uncertain significance ★ ⚠ same residue
ART1 p.Arg140= Benign ★★ same type
ART1 p.Leu43= Benign ★★ same type
ART1 p.Ala120Pro Uncertain significance ★ ⚠ same type
ART1 p.Ala133Val Uncertain significance ★ ⚠ same type
ART1 p.Ala138Val Uncertain significance ★ ⚠ same type
ART1 p.Ala161Ser Uncertain significance ★ ⚠ same type
ART1 p.Ala227Gly 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/art1-p-pro245ser (accessed [today's date]).

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