Is CRELD1 p.Met13= (c.37=) pathogenic?

CRELD1 p.Met13= (c.37=) is classified Benign in CRELD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-15). Absent from gnomAD v4.1; Associated with atrioventricular septal defect, susceptibility to, 2.

What condition is associated with CRELD1 p.Met13= (c.37=)?

CRELD1 p.Met13= (c.37=) is associated with atrioventricular septal defect, susceptibility to, 2 (ClinVar).

How common is CRELD1 p.Met13= (c.37=) in the general population?

CRELD1 p.Met13= (c.37=) is absent from gnomAD v4.1 (gnomAD).

CRELD1 p.Met13=

c.37= · rs279552 · VCV137033

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

atrioventricular septal defect, susceptibility to, 2

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 0.25	GERP -2, phastCons 0.01

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: CRELD1
Protein: p.Met13=
Coding: c.37=
MANE Select: NM_001077415
dbSNP: rs279552
Type: single nucleotide variant
Location: chr3:9934475 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.68
Residue 13: a UniProt-annotated variant site (in)

Full CRELD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

atrioventricular septal defect, susceptibility to, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CRELD1 p.Met13Val Benign/Likely benign ★★ same residue
CRELD1 c.1049-283C>T Uncertain significance ★★ same condition
CRELD1 c.1049-376T>G Uncertain significance ★★ same condition
CRELD1 c.1049-401C>T Uncertain significance ★★ same condition
CRELD1 p.Arg107Cys Uncertain significance ★★ ⚠ same condition
CRELD1 p.Arg175Gln Uncertain significance ★★ ⚠ same condition
CRELD1 p.Asn72Ser Uncertain significance ★★ ⚠ same condition
CRELD1 p.Cys221Arg 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/creld1-p-met13 (accessed [today's date]).

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