Is G6PD p.Pro415= (c.1245C>T) pathogenic?

G6PD p.Pro415= (c.1245C>T) is classified Conflicting classifications of pathogenicity in G6PD (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-16). Rare (popmax 0.179%, afr); Associated with anemia, nonspherocytic hemolytic, due to G6PD deficiency.

What condition is associated with G6PD p.Pro415= (c.1245C>T)?

G6PD p.Pro415= (c.1245C>T) is associated with anemia, nonspherocytic hemolytic, due to G6PD deficiency (ClinVar).

How common is G6PD p.Pro415= (c.1245C>T) in the general population?

G6PD p.Pro415= (c.1245C>T) is rare (popmax 0.179%, afr) (gnomAD).

G6PD p.Pro415=

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.1245C>T · rs147131392 · VCV193614

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.179%, afr)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -13	GERP -3.4
Overall
CADD	0.034	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.179% African / African-American · 103/57,580 alleles

Filtering AF 0.151% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.14%

Overall 0.0102% 124/1,211,109 alleles · rare exomes 62/1,098,192 · genomes 62/112,917 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.179%	559
Admixed American	0.0239%	4,176
Remaining individualsnot grpmax-eligible	0.0084%	11,909
European (non-Finnish)	0.00067%	149,233

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: G6PD
Protein: p.Pro415=
Coding: c.1245C>T
MANE Select: NM_001360016
dbSNP: rs147131392
Type: single nucleotide variant
Location: chrX:154532609 (GRCh38)
Structure: AlphaFold pLDDT 94.54 · 25 PDB
Residue 415: a β-strand

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.Cys415Arg Pathogenic/Likely pathogenic ★★ ⚠ same residue
G6PD p.Pro415Leu Uncertain significance ★ ⚠ same residue
G6PD p.Pro415Ser Uncertain significance ★ ⚠ 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
G6PD p.Ala74Gly Pathogenic/Likely 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-pro415 (accessed [today's date]).

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