Is CTRC p.Asn52= (c.156C>T) pathogenic?

CTRC p.Asn52= (c.156C>T) is classified Benign in CTRC (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Low-frequency (popmax 2.71%, afr); Associated with hereditary chronic pancreatitis.

What condition is associated with CTRC p.Asn52= (c.156C>T)?

CTRC p.Asn52= (c.156C>T) is associated with hereditary chronic pancreatitis (ClinVar).

How common is CTRC p.Asn52= (c.156C>T) in the general population?

CTRC p.Asn52= (c.156C>T) is low-frequency (popmax 2.71%, afr) (gnomAD).

CTRC p.Asn52=

Q: How is Autosomal dominant hereditary chronic pancreatitis inherited?

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

c.156C>T · rs77373944 · VCV292908

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.71%, afr)

Conditions

hereditary chronic pancreatitis

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 -13	GERP -5.2
Overall
CADD	0.093	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.71% African / African-American · 2,031/75,062 alleles

Filtering AF 2.61% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.57%

Overall 0.145% 2,347/1,614,206 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.71%	37
Admixed American	0.227%	441
Remaining individualsnot grpmax-eligible	0.174%	573
Middle Eastern	0.148%	674
South Asian	0.00878%	11,384
European (non-Finnish)	0.00449%	22,265
East Asian	0.00223%	44,882

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.Asn52=
Coding: c.156C>T
MANE Select: NM_007272
dbSNP: rs77373944
Type: single nucleotide variant
Location: chr1:15440516 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.03 · 1 PDB
Residue 52: a disulfide bond; the peptidase s1 domain

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.Asn52Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
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 c.356+1G>A Uncertain significance ★★ same condition
CTRC c.40+4A>G Uncertain significance ★★ same condition
CTRC c.40+6C>T Uncertain significance ★★ same condition
CTRC p.Ala12Val 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/ctrc-p-asn52 (accessed [today's date]).

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