Is CTRC p.Pro20fs (c.57dup) pathogenic?

CTRC p.Pro20fs (c.57dup) is classified Pathogenic in CTRC (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-16). Very rare (popmax 0.000195%, nfe); Associated with hereditary chronic pancreatitis.

What condition is associated with CTRC p.Pro20fs (c.57dup)?

CTRC p.Pro20fs (c.57dup) is associated with hereditary chronic pancreatitis (ClinVar).

How common is CTRC p.Pro20fs (c.57dup) in the general population?

CTRC p.Pro20fs (c.57dup) is very rare (popmax 0.000195%, nfe) (gnomAD).

CTRC p.Pro20fs

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

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

c.57dup · rs761774161 · VCV1749750

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000195%, nfe)

Conditions

hereditary chronic pancreatitis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.53	GERP -3.6, phastCons 0.039

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000195% European (non-Finnish) · 2/1,028,102 alleles

Filtering AF 3.2e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.2e-05%

Overall 0.000162% 2/1,230,830 alleles · very rare

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: CTRC
Protein: p.Pro20fs
Coding: c.57dup
MANE Select: NM_007272
dbSNP: rs761774161
Type: Duplication
Location: chr1:15440315 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.03 · 1 PDB
Residue 20: a disulfide bond

Full CTRC 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

CTRC p.Pro20Ser Uncertain significance ★★ ⚠ same residue
CTRC p.Ser210fs Likely pathogenic ★ same condition
CTRC p.Glu92fs Uncertain significance ★ same condition
CTRC c.41-3dup Likely benign ★ same condition
CTRC c.494-1G>C Pathogenic/Likely pathogenic ★★ same condition
CTRC p.Arg29Ter Pathogenic/Likely pathogenic ★★ same condition
CTRC p.Gln174Ter Pathogenic/Likely pathogenic ★★ same condition
CTRC p.Lys247_Arg254del 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/ctrc-p-pro20fs (accessed [today's date]).

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