Is AMPD1 p.Thr490= (c.1470C>T) pathogenic?

AMPD1 p.Thr490= (c.1470C>T) is classified Likely benign in AMPD1 (ClinVar, Single submitter, 1 submitter). Very rare (popmax 0.000254%, nfe); Associated with autism.

What condition is associated with AMPD1 p.Thr490= (c.1470C>T)?

AMPD1 p.Thr490= (c.1470C>T) is associated with autism (ClinVar).

How common is AMPD1 p.Thr490= (c.1470C>T) in the general population?

AMPD1 p.Thr490= (c.1470C>T) is very rare (popmax 0.000254%, nfe) (gnomAD).

AMPD1 p.Thr490=

c.1470C>T · rs587779371 · VCV91872

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

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 -0.14	GERP -0.29
Overall
CADD	5.519	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,038 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000205% 3/1,461,866 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: AMPD1
Protein: p.Thr490=
Coding: c.1470C>T
MANE Select: NM_000036
dbSNP: rs587779371
Type: single nucleotide variant
Location: chr1:114675922 (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.Thr490Asn Uncertain significance ★ ⚠ same residue
AMPD1 p.Thr490Ile Uncertain significance ★ ⚠ same residue
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

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-thr490 (accessed [today's date]).

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