CRELD2 p.Ser207=
c.621G>A · rs138811682 · VCV2653354
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.32%, nfe)
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 -9 | GERP -2.5 |
| Overall | ||
| CADD | 0.084 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.32%
European (non-Finnish) · 3,705/1,156,988 alleles
Filtering AF
0.312%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.308%
Overall
0.253%
3,965/1,569,722 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.32% | 312 |
| Remaining individualsnot grpmax-eligible | 0.281% | 356 |
| Admixed American | 0.0574% | 1,743 |
| African / African-American | 0.0573% | 1,745 |
| Finnishnot grpmax-eligible | 0.0183% | 5,457 |
| Middle Eastern | 0.0166% | 6,014 |
| South Asian | 0.00349% | 28,617 |
| East Asian | 0.00233% | 42,866 |
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
- CRELD2
- Protein
- p.Ser207=
- Coding
- c.621G>A
- MANE Select
- NM_024324
- dbSNP
- rs138811682
- Type
- single nucleotide variant
- Location
- chr22:49922640 (GRCh38)
- Gene constraint
- LOEUF 1.119 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.63
Similar variants
- CRELD2 p.Ser207Leu Uncertain significance ★ ⚠ same residue
- CRELD2 p.Ala236= Benign ★★ same type
- CRELD2 p.Cys294= Benign/Likely benign ★★ same type
- CRELD2 p.Gly162= Benign ★★ same type
- CRELD2 c.593-181G>T Uncertain significance ★ same type
- CRELD2 c.593-202A>T Uncertain significance ★ same type
- CRELD2 c.593-208G>T Uncertain significance ★ same type
- CRELD2 c.593-222C>T 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/creld2-p-ser207 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown