TF p.Cys615=
c.1845C>T · rs142894328 · VCV2957723
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 -2.2 | GERP -4.1 |
| Overall | ||
| CADD | 3.201 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,936 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.0013%
21/1,614,070 alleles · very rare
exomes 17/1,461,862 · genomes 4/152,208 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,489 |
| South Asian | 0.00549% | 18,218 |
| European (non-Finnish) | 0.000847% | 118,004 |
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
- TF
- Protein
- p.Cys615=
- Coding
- c.1845C>T
- MANE Select
- NM_001063
- dbSNP
- rs142894328
- Type
- single nucleotide variant
- Location
- chr3:133775590 (GRCh38)
- Gene constraint
- LOEUF 0.834 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.39 · 69 PDB
- Residue 615
- an α-helix; the transferrin-like 2 domain; a disulfide bond
Similar variants
- TF c.-18C>T Uncertain significance ★★ same type
- TF p.Ala318Ser Uncertain significance ★★ ⚠ same type
- TF p.Ala72Val Uncertain significance ★★ ⚠ same type
- TF p.Gln264Glu Uncertain significance ★★ ⚠ same type
- TF p.Gln559Leu Uncertain significance ★★ ⚠ same type
- TF p.Ile229Thr Uncertain significance ★★ ⚠ same type
- TF p.Thr112Ala Uncertain significance ★★ ⚠ same type
- TF p.Val270Asp 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/tf-p-cys615 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown