Is EPG5 p.Pro487= (c.1461C>T) pathogenic?

EPG5 p.Pro487= (c.1461C>T) is classified Benign/Likely benign in EPG5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-24). Rare (popmax 0.792%, eas); Associated with Vici syndrome.

What condition is associated with EPG5 p.Pro487= (c.1461C>T)?

EPG5 p.Pro487= (c.1461C>T) is associated with Vici syndrome (ClinVar).

How common is EPG5 p.Pro487= (c.1461C>T) in the general population?

EPG5 p.Pro487= (c.1461C>T) is rare (popmax 0.792%, eas) (gnomAD).

EPG5 p.Pro487=

c.1461C>T · rs142675465 · VCV712907

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.792%, eas)

Conditions

Vici syndrome

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 -9.5	GERP -2.9
Overall
CADD	2.047	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.792% East Asian · 355/44,838 alleles

Filtering AF 0.724% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.697%

Overall 0.0249% 401/1,612,790 alleles · rare exomes 345/1,460,752 · genomes 56/152,038 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.792%	126
Remaining individualsnot grpmax-eligible	0.04%	2,498
Middle Eastern	0.0331%	3,025
Admixed American	0.00667%	14,987
African / African-American	0.00267%	37,472
South Asian	0.0011%	90,946
European (non-Finnish)	0.00102%	98,267

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: EPG5
Protein: p.Pro487=
Coding: c.1461C>T
MANE Select: NM_020964
dbSNP: rs142675465
Type: single nucleotide variant
Location: chr18:45949520 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.24 · 1 PDB
Residue 487: a UniProt-annotated variant site (in vicis)

Full EPG5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Vici syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EPG5 c.1253-1G>A Pathogenic ★★ same condition
EPG5 c.1497+1G>T Pathogenic/Likely pathogenic ★★ same condition
EPG5 c.1678-1G>A Likely pathogenic ★★ same condition
EPG5 c.4475-1G>A Likely pathogenic ★★ same condition
EPG5 c.5304+1G>A Likely pathogenic ★★ same condition
EPG5 c.5869+1G>A Pathogenic ★★ same condition
EPG5 c.6049+5G>A Likely pathogenic ★★ same condition
EPG5 p.Arg1161Ter 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/epg5-p-pro487 (accessed [today's date]).

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