Is EPOR p.Asn487Ser (c.1460A>G) pathogenic?

EPOR p.Asn487Ser (c.1460A>G) is classified Benign/Likely benign in EPOR (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-04-01). AlphaMissense: likely benign (0.0873); Rare (popmax 0.767%, amr); Associated with primary familial polycythemia due to EPO receptor mutation.

What condition is associated with EPOR p.Asn487Ser (c.1460A>G)?

EPOR p.Asn487Ser (c.1460A>G) is associated with primary familial polycythemia due to EPO receptor mutation (ClinVar).

How common is EPOR p.Asn487Ser (c.1460A>G) in the general population?

EPOR p.Asn487Ser (c.1460A>G) is rare (popmax 0.767%, amr) (gnomAD).

How is Primary familial polycythemia inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about EPOR p.Asn487Ser (c.1460A>G)?

AlphaMissense predicts likely benign (score 0.0873) — an in-silico prediction, not a clinical call.

EPOR p.Asn487Ser

c.1460A>G · rs62638745 · VCV16598

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely benign

0.0873 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.767%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary familial polycythemia due to EPO receptor mutation

Computational evidence

Protein change
AlphaMissense	0.0873	likely benign
REVEL	0.036	moderately benign-leaning
SaProt	LLR -4.45	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.8	GERP 1.7, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 6,220 bp · p 0.0057 · regional, not allelic
Overall
CADD	19.34	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.767% Admixed American · 460/60,008 alleles

Filtering AF 0.709% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.686%

Overall 0.665% 10,729/1,614,018 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.91%	52
Admixed Americangrpmax	0.767%	130
European (non-Finnish)	0.703%	142
Remaining individualsnot grpmax-eligible	0.549%	182
Amishnot grpmax-eligible	0.44%	228
Middle Eastern	0.363%	276
South Asian	0.251%	398
Ashkenazi Jewishnot grpmax-eligible	0.186%	538
African / African-American	0.128%	781
East Asian	0.00223%	44,876

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: EPOR
Protein: p.Asn487Ser
Coding: c.1460A>G
MANE Select: NM_000121
dbSNP: rs62638745
Type: single nucleotide variant
Location: chr19:11378051 (GRCh38)
Gene constraint: LOEUF 0.787 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.74 · 22 PDB
Residue 487: a UniProt-annotated variant site (in ecyt1 and erythroleukemia); the 'disordered' region

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

Disease context

primary familial polycythemia due to EPO receptor mutation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary familial polycythemia (Orphanet):

Inheritance: Autosomal dominant
Onset: All ages

Similar variants

EPOR p.Trp439Ter Pathogenic ★★ same condition
EPOR p.Pro327Leu Uncertain significance ★★ ⚠ same condition
EPOR c.115+7A>G Benign/Likely benign ★★ same condition
EPOR c.-55G>A Benign ★★ same condition
EPOR c.*35G>A Benign ★★ same condition
EPOR p.Ala186= Benign/Likely benign ★★ same condition
EPOR p.Ala219= Benign ★★ same condition
EPOR p.Arg56= Benign/Likely benign ★★ 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/epor-p-asn487ser (accessed [today's date]).

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