TDRD7 p.Pro362=
c.1086G>A · VCV4903808
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
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 -7.4 | GERP -4.8 |
| Overall | ||
| CADD | 0.509 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/60,004 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00175%
Overall
0.00279%
45/1,614,054 alleles · very rare
exomes 38/1,461,840 · genomes 7/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 15,001 |
| African / African-American | 0.00534% | 18,734 |
| South Asian | 0.00329% | 30,361 |
| European (non-Finnish) | 0.0028% | 35,759 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
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
- TDRD7
- Protein
- p.Pro362=
- Coding
- c.1086G>A
- MANE Select
- NM_014290
- Type
- single nucleotide variant
- Location
- chr9:97460408 (GRCh38)
- Gene constraint
- LOEUF 0.521 · pLI 0.37 (gnomAD)
- Structure
- AlphaFold pLDDT 73.60 · 1 PDB
- Residue 362
- the hth ost-type 3 domain
Similar variants
- TDRD7 p.Ala651Thr Uncertain significance ★★ ⚠ same type
- TDRD7 p.Ala895Thr Uncertain significance ★★ ⚠ same type
- TDRD7 p.Ala958Thr Uncertain significance ★★ ⚠ same type
- TDRD7 p.Arg1013Gln Uncertain significance ★★ ⚠ same type
- TDRD7 p.Arg834Cys Uncertain significance ★★ ⚠ same type
- TDRD7 p.Arg99Cys Uncertain significance ★★ ⚠ same type
- TDRD7 p.Arg99His Uncertain significance ★★ ⚠ same type
- TDRD7 p.Asn631Ser Uncertain significance ★★ ⚠ 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/tdrd7-p-pro362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown