CEMIP p.Ser317=
c.951T>C · rs151251075 · VCV734680
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.47%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | donor gain, 13 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -4.5 |
| Overall | ||
| CADD | 6.123 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.47%
African / African-American · 1,100/75,002 alleles
Filtering AF
1.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.37%
Overall
0.0758%
1,223/1,614,006 alleles · low-frequency
exomes 584/1,461,778 · genomes 639/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.47% | 68 |
| Admixed American | 0.09% | 1,111 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Middle Eastern | 0.033% | 3,031 |
| European (non-Finnish) | 0.00153% | 65,551 |
| South Asian | 0.0011% | 91,070 |
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.Ser317=
- Coding
- c.951T>C
- MANE Select
- NM_001293298
- dbSNP
- rs151251075
- Type
- single nucleotide variant
- Location
- chr15:80888783 (GRCh38)
- Gene constraint
- LOEUF 0.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.69
- Residue 317
- the gg-type lectin 1 domain; the 'necessary for its endoplasmic reticulum (er) retention and interaction with hspa5' region
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-ser317 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown