Is CPA1 p.Phe206= (c.618C>T) pathogenic?

CPA1 p.Phe206= (c.618C>T) is classified Likely benign in CPA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-07). Absent from gnomAD v4.1.

How common is CPA1 p.Phe206= (c.618C>T) in the general population?

CPA1 p.Phe206= (c.618C>T) is absent from gnomAD v4.1 (gnomAD).

CPA1 p.Phe206=

c.618C>T · VCV3695232

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.014	GERP -4.7, phastCons 0.78
Overall
CADD	2.928	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CPA1
Protein: p.Phe206=
Coding: c.618C>T
MANE Select: NM_001868
Type: single nucleotide variant
Location: chr7:130383716 (GRCh38)
Gene constraint: LOEUF 1.14 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.41 · 6 PDB
Residue 206: the peptidase m14 domain; an α-helix

Full CPA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPA1 p.Phe206Leu Likely benign ★ same residue
CPA1 p.Asn256Lys Likely pathogenic ★★ same type
CPA1 p.Ser282Pro Pathogenic ★★ same type
CPA1 c.1072+1G>T Uncertain significance ★★ same type
CPA1 c.1073-1G>A Uncertain significance ★★ same type
CPA1 c.147+4A>C Uncertain significance ★★ same type
CPA1 c.586-2A>G Uncertain significance ★★ same type
CPA1 c.696+5C>T Uncertain significance ★★ 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/cpa1-p-phe206 (accessed [today's date]).

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