Is EP400 p.Pro1701= (c.5103G>A) pathogenic?

EP400 p.Pro1701= (c.5103G>A) is classified Benign/Likely benign in EP400 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-03-01). Rare (popmax 0.868%, nfe).

How common is EP400 p.Pro1701= (c.5103G>A) in the general population?

EP400 p.Pro1701= (c.5103G>A) is rare (popmax 0.868%, nfe) (gnomAD).

EP400 p.Pro1701=

c.5103G>A · rs116870851 · VCV771187

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.868%, nfe)

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 -7.5	GERP -3.1
Overall
CADD	0.06	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.868% European (non-Finnish) · 10,229/1,178,460 alleles

Filtering AF 0.854% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.848%

Overall 0.785% 12,647/1,611,216 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.64%	38
European (non-Finnish)grpmax	0.868%	115
Remaining individualsnot grpmax-eligible	0.601%	166
Ashkenazi Jewishnot grpmax-eligible	0.398%	251
Admixed American	0.131%	766
African / African-American	0.116%	862
South Asian	0.0772%	1,296
Middle Eastern	0.0662%	1,512
East Asian	0.0112%	8,966

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: EP400
Protein: p.Pro1701=
Coding: c.5103G>A
MANE Select: NM_015409
dbSNP: rs116870851
Type: single nucleotide variant
Location: chr12:132027525 (GRCh38)
Gene constraint: LOEUF 0.365 · pLI 1.00 (gnomAD)

Full EP400 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EP400 p.Thr664Ala Uncertain significance ★★ same type
EP400 c.1435+8G>A Benign ★★ same type
EP400 c.7027-9C>T Benign ★★ same type
EP400 p.Ala146= Likely benign ★★ same type
EP400 p.Ala1649Thr Benign/Likely benign ★★ same type
EP400 p.Ala1764= Benign ★★ same type
EP400 p.Ala244= Likely benign ★★ same type
EP400 p.Ala2803= 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/ep400-p-pro1701 (accessed [today's date]).

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