Is CREG1 p.Ser44= (c.132C>T) pathogenic?

CREG1 p.Ser44= (c.132C>T) is classified Likely benign in CREG1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-12). Rare (popmax 0.638%, eas); Associated with CREG1-related disorder.

What condition is associated with CREG1 p.Ser44= (c.132C>T)?

CREG1 p.Ser44= (c.132C>T) is associated with CREG1-related disorder (ClinVar).

How common is CREG1 p.Ser44= (c.132C>T) in the general population?

CREG1 p.Ser44= (c.132C>T) is rare (popmax 0.638%, eas) (gnomAD).

CREG1 p.Ser44=

c.132C>T · rs547663782 · VCV3060330

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.638%, eas)

Conditions

CREG1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Overall
CADD	7.727	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.638% East Asian · 208/32,612 alleles

Filtering AF 0.567% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.539%

Overall 0.015% 211/1,410,552 alleles · rare exomes 200/1,258,376 · genomes 11/152,176 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.638%	157
Remaining individualsnot grpmax-eligible	0.00555%	18,029

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: CREG1
Protein: p.Ser44=
Coding: c.132C>T
MANE Select: NM_003851
dbSNP: rs547663782
Type: single nucleotide variant
Location: chr1:167553610 (GRCh38)
Gene constraint: LOEUF 1.795 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.08 · 1 PDB

Full CREG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CREG1-related disorder

Similar variants

CREG1 p.Ser44Phe Uncertain significance ★ ⚠ same residue
CREG1 p.Phe85= Likely benign same condition
CREG1 p.Ala11Val Uncertain significance ★ ⚠ same type
CREG1 p.Ala130Ser Uncertain significance ★ ⚠ same type
CREG1 p.Ala15Thr Uncertain significance ★ ⚠ same type
CREG1 p.Ala18Ser Uncertain significance ★ ⚠ same type
CREG1 p.Ala23Val Uncertain significance ★ ⚠ same type
CREG1 p.Ala29Ser 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/creg1-p-ser44 (accessed [today's date]).

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