Is EPG5 p.Pro1663= (c.4989T>G) pathogenic?

EPG5 p.Pro1663= (c.4989T>G) is classified Likely benign in EPG5 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-22). Ultra-rare (popmax 0.0653%, eas); Associated with Vici syndrome.

What condition is associated with EPG5 p.Pro1663= (c.4989T>G)?

EPG5 p.Pro1663= (c.4989T>G) is associated with Vici syndrome (ClinVar).

How common is EPG5 p.Pro1663= (c.4989T>G) in the general population?

EPG5 p.Pro1663= (c.4989T>G) is ultra-rare (popmax 0.0653%, eas) (gnomAD).

EPG5 p.Pro1663=

c.4989T>G · rs759914920 · VCV1652553

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0653%, 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 0.006	GERP 0.61, phastCons 0.021
Overall
CADD	6.387	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0653% East Asian · 29/44,382 alleles

Filtering AF 0.0467% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0404%

Overall 0.00201% 32/1,593,804 alleles · ultra-rare exomes 25/1,441,596 · genomes 7/152,208 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0653%	1,530
Remaining individualsnot grpmax-eligible	0.00327%	30,625
African / African-American	0.00134%	74,616

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.Pro1663=
Coding: c.4989T>G
MANE Select: NM_020964
dbSNP: rs759914920
Type: single nucleotide variant
Location: chr18:45887871 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.24 · 1 PDB
Residue 1663: a UniProt-annotated variant site (in vicis); a UniProt-annotated variant site (in nedpam)

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 p.Pro1663Leu Uncertain significance ★ ⚠ same residue
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

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-pro1663 (accessed [today's date]).

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