Is AMPD1 p.Pro201= (c.603T>A) pathogenic?

AMPD1 p.Pro201= (c.603T>A) is classified Likely benign in AMPD1 (ClinVar, Single submitter, 1 submitter). Absent from gnomAD v4.1; Associated with autism.

What condition is associated with AMPD1 p.Pro201= (c.603T>A)?

AMPD1 p.Pro201= (c.603T>A) is associated with autism (ClinVar).

How common is AMPD1 p.Pro201= (c.603T>A) in the general population?

AMPD1 p.Pro201= (c.603T>A) is absent from gnomAD v4.1 (gnomAD).

AMPD1 p.Pro201=

c.603T>A · rs587779377 · VCV91880

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

autism

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.9	GERP -5.2
Overall
CADD	2.815	PHRED · no single calibrated threshold — expert panels disagree

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: AMPD1
Protein: p.Pro201=
Coding: c.603T>A
MANE Select: NM_000036
dbSNP: rs587779377
Type: single nucleotide variant
Location: chr1:114680423 (GRCh38)
Gene constraint: LOEUF 1.036 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.84

Full AMPD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autism — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AMPD1 p.Arg467Cys Uncertain significance ★★ ⚠ same condition
AMPD1 p.Asp170Val Uncertain significance ★★ ⚠ same condition
AMPD1 p.Asp243Asn Uncertain significance ★★ ⚠ same condition
AMPD1 p.Ile169Met Uncertain significance ★★ ⚠ same condition
AMPD1 c.-30G>A Uncertain significance ★ ⚠ same condition
AMPD1 c.-69C>G Uncertain significance ★ ⚠ same condition
AMPD1 p.Cys450Trp Uncertain significance ★ same condition
AMPD1 p.Pro539Ser 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/ampd1-p-pro201 (accessed [today's date]).

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