MCTP2 p.Ser69=
c.207C>T · rs147356828 · VCV708180
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.46%, 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 -20 | GERP -4.2 |
| Overall | ||
| CADD | 0.037 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.46%
East Asian · 656/44,868 alleles
Filtering AF
1.37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.33%
Overall
0.0458%
739/1,614,088 alleles · low-frequency
exomes 688/1,461,756 · genomes 51/152,332 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.46% | 68 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Finnishnot grpmax-eligible | 0.00781% | 12,805 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00314% | 31,892 |
| Admixed American | 0.00167% | 60,014 |
| African / African-American | 0.00133% | 75,058 |
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.Ser69=
- Coding
- c.207C>T
- MANE Select
- NM_001385001
- dbSNP
- rs147356828
- Type
- single nucleotide variant
- Location
- chr15:94298472 (GRCh38)
- Gene constraint
- LOEUF 1.328 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.73 · 1 PDB
- Residue 69
- the 'disordered' region
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-ser69 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown