MCTP2 p.Ser336=
c.1008C>T · rs200476577 · VCV748458
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0286%, afr)
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 -0.085 | GERP 0.15, phastCons 0.52 |
| Overall | ||
| CADD | 12.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0286%
African / African-American · 21/73,384 alleles
Filtering AF
0.0191%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.00164%
26/1,583,188 alleles · ultra-rare
exomes 8/1,431,052 · genomes 18/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0286% | 3,494 |
| Admixed American | 0.00531% | 18,834 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,096 |
| European (non-Finnish) | 8.58e-05% | 1,165,524 |
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.Ser336=
- Coding
- c.1008C>T
- MANE Select
- NM_001385001
- dbSNP
- rs200476577
- Type
- single nucleotide variant
- Location
- chr15:94356139 (GRCh38)
- Gene constraint
- LOEUF 1.328 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.73 · 1 PDB
- Residue 336
- the c2 2 domain
Similar variants
- 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
- MCTP2 p.Ala877Thr Benign ★★ same type
- MCTP2 p.Arg340His 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-ser336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown