Is EPX p.Asn211Ser (c.632A>G) pathogenic?

EPX p.Asn211Ser (c.632A>G) is classified Likely benign in EPX (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-16). AlphaMissense: likely benign (0.0503); Rare (popmax 0.181%, mid).

How common is EPX p.Asn211Ser (c.632A>G) in the general population?

EPX p.Asn211Ser (c.632A>G) is rare (popmax 0.181%, mid) (gnomAD).

What do computational predictors say about EPX p.Asn211Ser (c.632A>G)?

AlphaMissense predicts likely benign (score 0.0503) — an in-silico prediction, not a clinical call.

EPX p.Asn211Ser

c.632A>G · rs148671148 · VCV3090009

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0503 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.181%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0503	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -0.79	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 -0.73	GERP -4.3
Regional constraint	o/e 0.98	unconstrained · MANE · 12 kb · p 0.44 · regional, not allelic
Overall
CADD	0.257	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 0.181% Middle Eastern · 11/6,084 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0784%

Overall 0.0109% 176/1,613,964 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.181%	553
East Asian	0.0535%	1,871
Remaining individualsnot grpmax-eligible	0.0112%	8,926
European (non-Finnish)	0.0102%	9,833
Admixed American	0.00833%	11,999
South Asian	0.00769%	13,012
African / African-American	0.00267%	37,443

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: EPX
Protein: p.Asn211Ser
Coding: c.632A>G
MANE Select: NM_000502
dbSNP: rs148671148
Type: single nucleotide variant
Location: chr17:58195001 (GRCh38)
Gene constraint: LOEUF 0.984 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.40 · 1 PDB
Residue 211: an α-helix

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

Similar variants

EPX p.Asn211Lys Uncertain significance ★ ⚠ same residue
EPX c.170+5A>G Likely benign ★★ same type
EPX c.464+8C>T Benign ★★ same type
EPX c.801+1G>A Likely benign ★★ same type
EPX p.Asn572Tyr Benign ★★ same type
EPX p.Cys257Ter Benign ★★ same type
EPX p.Leu624= Benign/Likely benign ★★ same type
EPX p.Phe308Leu 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/epx-p-asn211ser (accessed [today's date]).

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