TMEM216 p.Pro10=
c.30G>A · rs1590641170 · VCV790362
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00246%, eas)
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 6.5 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 15.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00246%
East Asian · 1/40,714 alleles
Overall
6.52e-05%
1/1,534,054 alleles · very rare
exomes 1/1,381,860 · genomes 0/152,194 · joint denominator
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
- TMEM216
- Protein
- p.Pro10=
- Coding
- c.30G>A
- MANE Select
- NM_001173990
- dbSNP
- rs1590641170
- Type
- single nucleotide variant
- Location
- chr11:61392661 (GRCh38)
- Gene constraint
- LOEUF 1.453 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 89.18
Similar variants
- TMEM216 c.137-1G>A Likely pathogenic ★★ same type
- TMEM216 c.137-2A>G Likely pathogenic ★★ same type
- TMEM216 c.229+1G>A Likely pathogenic ★★ same type
- TMEM216 c.229+1G>C Likely pathogenic ★★ same type
- TMEM216 c.230-2A>G Likely pathogenic ★★ same type
- TMEM216 c.34+2T>C Likely pathogenic ★★ same type
- TMEM216 c.-69G>A Pathogenic ★★ same type
- TMEM216 c.-69G>T Pathogenic ★★ 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/tmem216-p-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown