TENM3 p.Asp2445=
c.7335T>C · rs200218318 · VCV3042630
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0541%, amr)
Conditions
1
TENM3-related disorder
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 -2.5 | GERP -4.9 |
| Overall | ||
| CADD | 0.875 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0541%
Admixed American · 32/59,096 alleles
Filtering AF
0.0393%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0344%
Overall
0.00342%
55/1,607,120 alleles · ultra-rare
exomes 31/1,454,824 · genomes 24/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0541% | 1,847 |
| Middle Eastern | 0.0165% | 6,050 |
| African / African-American | 0.0133% | 7,497 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,467 |
| South Asian | 0.00112% | 89,506 |
| European (non-Finnish) | 0.00051% | 196,076 |
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
- TENM3
- Protein
- p.Asp2445=
- Coding
- c.7335T>C
- MANE Select
- NM_001080477
- dbSNP
- rs200218318
- Type
- single nucleotide variant
- Location
- chr4:182796758 (GRCh38)
- Gene constraint
- LOEUF 0.305 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 77.76
- Residue 2445
- a UniProt-annotated variant site (in mcops15)
Disease context
TENM3-related disorder
Similar variants
- TENM3 p.Gln2247Ter Likely pathogenic ★ same condition
- TENM3 c.1639+9G>T Likely benign same condition
- TENM3 c.2585+9T>G Likely benign same condition
- TENM3 c.3862+5C>T Likely benign same condition
- TENM3 p.Leu1587= Likely benign same condition
- TENM3 p.Leu1595= Likely benign same condition
- TENM3 p.Leu2170= Likely benign same condition
- TENM3 p.Pro1266= Likely benign same condition
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/tenm3-p-asp2445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown