TERF2IP p.Val239=
c.717G>A · rs201847682 · VCV1757520
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0223%, 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 1.7 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 5.424 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0223%
East Asian · 10/44,874 alleles
Filtering AF
0.012%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00917%
Overall
0.00105%
17/1,614,014 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,487 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
| South Asian | 0.0011% | 91,082 |
| European (non-Finnish) | 0.000424% | 235,985 |
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
- TERF2IP
- Protein
- p.Val239=
- Coding
- c.717G>A
- MANE Select
- NM_018975
- dbSNP
- rs201847682
- Type
- single nucleotide variant
- Location
- chr16:75654319 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.76 · 5 PDB
- Residue 239
- the 'disordered' region
Similar variants
- TERF2IP p.Val239Met Uncertain significance ★ ⚠ same residue
- TERF2IP p.Ala123Gly Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala200Gly Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala387Val Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala61Thr Uncertain significance ★★ ⚠ same type
- TERF2IP p.Ala65Thr Uncertain significance ★★ ⚠ same type
- TERF2IP p.Arg133Gln Uncertain significance ★★ ⚠ same type
- TERF2IP p.Arg378Ser 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/terf2ip-p-val239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown