GTF2F2 p.Asp172=
c.516C>T · VCV3856221
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0154%, sas)
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 -1.6 | GERP -5.5 |
| Overall | ||
| CADD | 8.255 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0154%
South Asian · 14/90,960 alleles
Filtering AF
0.00921%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00736%
Overall
0.00806%
130/1,612,500 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0154% | 6,497 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,397 |
| Admixed American | 0.01% | 9,981 |
| European (non-Finnish) | 0.0084% | 11,910 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,605 |
| African / African-American | 0.00267% | 37,466 |
| East Asian | 0.00223% | 44,840 |
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
- GTF2F2
- Protein
- p.Asp172=
- Coding
- c.516C>T
- MANE Select
- NM_004128
- Type
- single nucleotide variant
- Location
- chr13:45267262 (GRCh38)
- Gene constraint
- LOEUF 1.94 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 82.92 · 63 PDB
- Residue 172
- an α-helix
Similar variants
- GTF2F2 p.Ala178Gly Uncertain significance ★ ⚠ same type
- GTF2F2 p.Arg177Leu Uncertain significance ★ ⚠ same type
- GTF2F2 p.Arg44Gln Uncertain significance ★ ⚠ same type
- GTF2F2 p.Arg44Trp Uncertain significance ★ ⚠ same type
- GTF2F2 p.Arg51Lys Uncertain significance ★ ⚠ same type
- GTF2F2 p.Asn158Ser Uncertain significance ★ ⚠ same type
- GTF2F2 p.Asp185Asn Uncertain significance ★ ⚠ same type
- GTF2F2 p.Asp204Val 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/gtf2f2-p-asp172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown