Is EPO p.Val3= (c.9G>A) pathogenic?

EPO p.Val3= (c.9G>A) is classified Likely benign in EPO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-06). Very rare (popmax 0.00352%, nfe); Associated with EPO-related disorder.

What condition is associated with EPO p.Val3= (c.9G>A)?

EPO p.Val3= (c.9G>A) is associated with EPO-related disorder (ClinVar).

How common is EPO p.Val3= (c.9G>A) in the general population?

EPO p.Val3= (c.9G>A) is very rare (popmax 0.00352%, nfe) (gnomAD).

EPO p.Val3=

c.9G>A · rs759518255 · VCV3043637

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00352%, nfe)

Conditions

EPO-related disorder

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 3.4	GERP -0.56, phastCons 0.92
Overall
CADD	7.877	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00352% European (non-Finnish) · 41/1,164,790 alleles

Filtering AF 0.00262% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00236%

Overall 0.00272% 43/1,579,506 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00352%	28,409
South Asian	0.0023%	43,479

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: EPO
Protein: p.Val3=
Coding: c.9G>A
MANE Select: NM_003254 · reported on NM_000799
dbSNP: rs759518255
Type: single nucleotide variant
Location: chr7:100720989 (GRCh38)
Structure: AlphaFold pLDDT 90.09 · 13 PDB

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

Disease context

EPO-related disorder

Similar variants

EPO p.Pro7Ser Uncertain significance ★ ⚠ same condition
EPO c.-136G>A Uncertain significance same condition
EPO p.Arg137Gln Uncertain significance ⚠ same condition
EPO p.Ser147Pro Uncertain significance ⚠ same condition
EPO p.Glu116= Likely benign same condition
EPO c.*8del Likely benign same condition
EPO c.14-1G>C Uncertain significance ★★ same type
EPO c.13+10C>T Benign/Likely benign ★★ 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/epo-p-val3 (accessed [today's date]).

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