CEMIP p.Pro1273=
c.3819A>G · rs116794418 · VCV781177
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.07%, 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 -8.3 | GERP -4.8 |
| Overall | ||
| CADD | 0.125 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.07%
African / African-American · 1,550/75,048 alleles
Filtering AF
1.98%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.95%
Overall
0.111%
1,792/1,614,208 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.07% | 48 |
| Admixed American | 0.193% | 517 |
| Remaining individualsnot grpmax-eligible | 0.162% | 619 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00102% | 98,337 |
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.Pro1273=
- Coding
- c.3819A>G
- MANE Select
- NM_001293298
- dbSNP
- rs116794418
- Type
- single nucleotide variant
- Location
- chr15:80943064 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.69
- Residue 1273
- 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-pro1273 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown