Is CPA1 p.Phe20= (c.60T>C) pathogenic?

CPA1 p.Phe20= (c.60T>C) is classified Likely benign in CPA1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-20). Absent from gnomAD v4.1; Associated with hereditary chronic pancreatitis.

What condition is associated with CPA1 p.Phe20= (c.60T>C)?

CPA1 p.Phe20= (c.60T>C) is associated with hereditary chronic pancreatitis (ClinVar).

How common is CPA1 p.Phe20= (c.60T>C) in the general population?

CPA1 p.Phe20= (c.60T>C) is absent from gnomAD v4.1 (gnomAD).

CPA1 p.Phe20=

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.60T>C · rs2536002910 · VCV1751623

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,312,528)

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.49	GERP -2.5, phastCons 1
Overall
CADD	9.182	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,312,528). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CPA1
Protein: p.Phe20=
Coding: c.60T>C
MANE Select: NM_001868
dbSNP: rs2536002910
Type: single nucleotide variant
Location: chr7:130380580 (GRCh38)
Gene constraint: LOEUF 1.14 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.41 · 6 PDB

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

Disease context

hereditary chronic pancreatitis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Autosomal dominant hereditary chronic pancreatitis (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Childhood
Prevalence: 1-9 / 1 000 000 (France)

Similar variants

CPA1 c.1072+1G>T Uncertain significance ★★ same condition
CPA1 c.147+4A>C Uncertain significance ★★ same condition
CPA1 c.586-2A>G Uncertain significance ★★ same condition
CPA1 c.696+5C>T Uncertain significance ★★ same condition
CPA1 p.Ala111Glu Uncertain significance ★★ ⚠ same condition
CPA1 p.Ala120Thr Uncertain significance ★★ ⚠ same condition
CPA1 p.Ala193Ser Uncertain significance ★★ ⚠ same condition
CPA1 p.Ala259Ser Uncertain significance ★★ ⚠ 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/cpa1-p-phe20 (accessed [today's date]).

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