Is APRT p.Ile13Met (c.39C>G) pathogenic?

APRT p.Ile13Met (c.39C>G) is classified Uncertain significance in APRT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-28). AlphaMissense: ambiguous (0.4973); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with APRT p.Ile13Met (c.39C>G)?

APRT p.Ile13Met (c.39C>G) is associated with Inborn genetic diseases (ClinVar).

How common is APRT p.Ile13Met (c.39C>G) in the general population?

APRT p.Ile13Met (c.39C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APRT p.Ile13Met (c.39C>G)?

AlphaMissense predicts ambiguous (score 0.4973) — an in-silico prediction, not a clinical call.

APRT p.Ile13Met

c.39C>G · VCV3887114

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4973 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4973	ambiguous
REVEL	0.659	pathogenic-leaning
SaProt	LLR -10.47	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.4	GERP 1.1, phastCons 1
Regional constraint	o/e 1.26	unconstrained · MANE · 2,198 bp · p 5.8e-05 · regional, not allelic
Overall
CADD	24.3	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APRT
Protein: p.Ile13Met
Coding: c.39C>G
MANE Select: NM_000485
Type: single nucleotide variant
Location: chr16:88811861 (GRCh38)
Gene constraint: LOEUF 1.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.91 · 16 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

APRT p.Ala138Thr Uncertain significance ★★ ⚠ same condition
APRT p.Arg89Trp Uncertain significance ★★ ⚠ same condition
APRT p.Asp59Asn Uncertain significance ★★ ⚠ same condition
APRT p.Ile61Val Uncertain significance ★★ ⚠ same condition
APRT p.Leu129Arg Uncertain significance ★★ ⚠ same condition
APRT p.Pro17Ala Uncertain significance ★★ ⚠ same condition
APRT p.Ala116Val Uncertain significance ★ ⚠ same condition
APRT p.Asp3Gly Uncertain significance ★ ⚠ same condition

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/aprt-p-ile13met (accessed [today's date]).

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