MCTP2 p.Pro398=
c.1194G>A · rs78373056 · VCV731413
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.294%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 14.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.294%
East Asian · 132/44,850 alleles
Filtering AF
0.253%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.238%
Overall
0.0165%
267/1,613,422 alleles · rare
exomes 215/1,461,126 · genomes 52/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.294% | 340 |
| South Asian | 0.0681% | 1,469 |
| Remaining individualsnot grpmax-eligible | 0.0608% | 1,644 |
| African / African-American | 0.008% | 12,501 |
| European (non-Finnish) | 0.00237% | 42,125 |
| Admixed American | 0.00167% | 59,980 |
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
- MCTP2
- Protein
- p.Pro398=
- Coding
- c.1194G>A
- MANE Select
- NM_001385001
- dbSNP
- rs78373056
- Type
- single nucleotide variant
- Location
- chr15:94358505 (GRCh38)
- Gene constraint
- LOEUF 1.328 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.73 · 1 PDB
- Residue 398
- the c2 2 domain
Similar variants
- MCTP2 p.Pro398Leu Uncertain significance ★ ⚠ same residue
- MCTP2 p.Pro398Thr Uncertain significance ★ ⚠ same residue
- MCTP2 p.Ala615Thr Uncertain significance ★★ ⚠ same type
- MCTP2 p.Thr227Met Uncertain significance ★★ ⚠ same type
- MCTP2 c.1583-6T>C Benign ★★ same type
- MCTP2 c.970-10A>G Likely benign ★★ same type
- MCTP2 p.Ala60Thr Benign ★★ same type
- MCTP2 p.Ala695Thr 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/mctp2-p-pro398 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown