CEMIP p.Val1259=
c.3777G>A · rs35526763 · VCV708970
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.56%, afr)
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 1.3 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 7.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.56%
African / African-American · 3,422/75,042 alleles
Filtering AF
4.43%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.38%
Overall
0.45%
7,263/1,614,202 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.56% | 22 |
| Middle Eastern | 3.56% | 28 |
| Admixed American | 0.906% | 110 |
| Remaining individualsnot grpmax-eligible | 0.725% | 138 |
| Ashkenazi Jewishnot grpmax-eligible | 0.692% | 144 |
| European (non-Finnish) | 0.199% | 503 |
| South Asian | 0.079% | 1,265 |
| Finnishnot grpmax-eligible | 0.00781% | 12,809 |
| East Asian | 0.00223% | 44,874 |
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
- CEMIP
- Protein
- p.Val1259=
- Coding
- c.3777G>A
- MANE Select
- NM_001293298
- dbSNP
- rs35526763
- Type
- single nucleotide variant
- Location
- chr15:80943022 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.69
- Residue 1259
- the gg-type lectin 2 domain
Similar variants
- CEMIP p.Ala33Val Uncertain significance ★★ ⚠ same type
- CEMIP p.Gly870Asp Uncertain significance ★★ ⚠ same type
- CEMIP c.1086+82T>A Benign ★★ same type
- CEMIP c.1087-239G>A Benign ★★ same type
- CEMIP c.1412-76G>A Benign ★★ same type
- CEMIP c.1587+57A>G Benign ★★ same type
- CEMIP c.1587+79G>A Benign ★★ same type
- CEMIP c.1797+102T>C 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/cemip-p-val1259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown