CECR2 p.His738=
c.2214T>C · rs41277560 · VCV774535
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.34%, 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 -3.6 | GERP -3.8 |
| Overall | ||
| CADD | 0.073 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.34%
European (non-Finnish) · 15,807/1,179,818 alleles
Filtering AF
1.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.32%
Overall
1.09%
17,627/1,613,674 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.34% | 75 |
| Remaining individualsnot grpmax-eligible | 1.09% | 91 |
| Admixed American | 0.663% | 151 |
| African / African-American | 0.545% | 183 |
| South Asian | 0.204% | 490 |
| Finnishnot grpmax-eligible | 0.204% | 491 |
| Middle Eastern | 0.066% | 1,515 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,699 |
| East Asian | 0.00446% | 22,436 |
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
- CECR2
- Protein
- p.His738=
- Coding
- c.2214T>C
- MANE Select
- NM_001290047
- dbSNP
- rs41277560
- Type
- single nucleotide variant
- Location
- chr22:17542357 (GRCh38)
- Gene constraint
- LOEUF 0.259 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.01 · 3 PDB
Similar variants
- CECR2 c.955-8C>T Benign ★★ same type
- CECR2 p.Ala743Val Benign ★★ same type
- CECR2 p.Ala847= Benign ★★ same type
- CECR2 p.Leu301Val Benign ★★ same type
- CECR2 p.Pro1063= Benign ★★ same type
- CECR2 p.Pro1323= Benign ★★ same type
- CECR2 p.Pro682Thr Likely benign ★★ ⚠ same type
- CECR2 p.Ser1437= Benign ★★ 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/cecr2-p-his738 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown