Is AMPD3 p.Phe501= (c.1503C>T) pathogenic?

AMPD3 p.Phe501= (c.1503C>T) is classified Benign in AMPD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-01-27). Rare (popmax 0.727%, afr).

How common is AMPD3 p.Phe501= (c.1503C>T) in the general population?

AMPD3 p.Phe501= (c.1503C>T) is rare (popmax 0.727%, afr) (gnomAD).

AMPD3 p.Phe501=

c.1503C>T · rs78473994 · VCV166686

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.727%, afr)

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	GERP -4.8
Overall
CADD	2.496	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.727% African / African-American · 545/75,014 alleles

Filtering AF 0.676% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.656%

Overall 0.0364% 587/1,614,130 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.727%	138
Admixed American	0.0367%	2,728
Remaining individualsnot grpmax-eligible	0.032%	3,125

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: AMPD3
Protein: p.Phe501=
Coding: c.1503C>T
MANE Select: NM_001025389
dbSNP: rs78473994
Type: single nucleotide variant
Location: chr11:10496884 (GRCh38)
Gene constraint: LOEUF 0.817 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.74

Full AMPD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AMPD3 c.1135-5C>A Uncertain significance ★★ same type
AMPD3 c.1135-6C>G Uncertain significance ★★ same type
AMPD3 c.1267-3C>T Uncertain significance ★★ same type
AMPD3 c.*287T>C Uncertain significance ★★ same type
AMPD3 c.*75C>T Uncertain significance ★★ same type
AMPD3 p.Ala141= Uncertain significance ★★ same type
AMPD3 p.Arg426Trp Uncertain significance ★★ ⚠ same type
AMPD3 p.Arg576= 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/ampd3-p-phe501 (accessed [today's date]).

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