Is EPPK1 p.Asp1164= (c.3492C>T) pathogenic?

EPPK1 p.Asp1164= (c.3492C>T) is classified Likely benign in EPPK1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-05-06). Ultra-rare (popmax 0.0578%, amr); Associated with EPPK1-related disorder.

What condition is associated with EPPK1 p.Asp1164= (c.3492C>T)?

EPPK1 p.Asp1164= (c.3492C>T) is associated with EPPK1-related disorder (ClinVar).

How common is EPPK1 p.Asp1164= (c.3492C>T) in the general population?

EPPK1 p.Asp1164= (c.3492C>T) is ultra-rare (popmax 0.0578%, amr) (gnomAD).

EPPK1 p.Asp1164=

c.3492C>T · rs373279236 · VCV3052192

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0578%, amr)

Conditions

EPPK1-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 -2.4	GERP -3.4
Overall
CADD	1.765	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0578% Admixed American · 34/58,798 alleles

Filtering AF 0.0425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0372%

Overall 0.0253% 406/1,602,906 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0578%	1,729
Remaining individualsnot grpmax-eligible	0.0306%	3,269
European (non-Finnish)	0.0278%	3,595
African / African-American	0.0201%	4,978
South Asian	0.0124%	8,096

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: EPPK1
Protein: p.Asp1164=
Coding: c.3492C>T
MANE Select: NM_031308
dbSNP: rs373279236
Type: single nucleotide variant
Location: chr8:143869762 (GRCh38)
Gene constraint: LOEUF 1.929 · pLI 0.12 (gnomAD)

Full EPPK1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EPPK1-related disorder

Similar variants

EPPK1 p.Gln2020Arg Uncertain significance ★ ⚠ same condition
EPPK1 p.Glu140Ter Uncertain significance ★ same condition
EPPK1 p.Pro35Thr Uncertain significance ★ ⚠ same condition
EPPK1 p.Val104Leu Uncertain significance ★ ⚠ same condition
EPPK1 p.Ala2265= Likely benign ★ same condition
EPPK1 p.Arg2218= Likely benign ★ same condition
EPPK1 p.Arg2305= Likely benign ★ same condition
EPPK1 p.Arg2356= 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/eppk1-p-asp1164 (accessed [today's date]).

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