Is G6PD p.Pro489= (c.1467C>A) pathogenic?

G6PD p.Pro489= (c.1467C>A) is classified Likely benign in G6PD (ClinVar, Single submitter, 1 submitter; last evaluated 2019-05-04). No allele count reported in gnomAD v4.1 (AN 1,209,383); Associated with anemia, nonspherocytic hemolytic, due to G6PD deficiency.

What condition is associated with G6PD p.Pro489= (c.1467C>A)?

G6PD p.Pro489= (c.1467C>A) is associated with anemia, nonspherocytic hemolytic, due to G6PD deficiency (ClinVar).

How common is G6PD p.Pro489= (c.1467C>A) in the general population?

G6PD p.Pro489= (c.1467C>A) is no allele count reported in gnomAD v4.1 (AN 1,209,383) (gnomAD).

G6PD p.Pro489=

Q: How is Class I glucose-6-phosphate dehydrogenase deficiency inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1467C>A · rs2148328181 · VCV1079997

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,209,383)

Conditions

anemia, nonspherocytic hemolytic, due to G6PD deficiency

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 -2.1	GERP -3.1
Overall
CADD	0.143	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,209,383). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: G6PD
Protein: p.Pro489=
Coding: c.1467C>A
MANE Select: NM_001360016
dbSNP: rs2148328181
Type: single nucleotide variant
Location: chrX:154532081 (GRCh38)
Structure: AlphaFold pLDDT 94.54 · 25 PDB

Full G6PD gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

anemia, nonspherocytic hemolytic, due to G6PD deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Class I glucose-6-phosphate dehydrogenase deficiency (Orphanet):

Inheritance: X-linked recessive
Onset: Neonatal
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

G6PD p.Arg489Leu Pathogenic ★★ same residue
G6PD p.Arg489Pro Pathogenic ★★ same residue
G6PD p.Pro489Ser Pathogenic ★★ same residue
G6PD p.Pro489Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
G6PD p.Ala335Asp Pathogenic/Likely pathogenic ★★ ⚠ same condition
G6PD p.Ala365Thr Pathogenic ★★ ⚠ same condition
G6PD p.Ala391Val Likely pathogenic ★★ same condition
G6PD p.Ala44Thr Pathogenic ★★ ⚠ 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/g6pd-p-pro489 (accessed [today's date]).

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