ZNF142 p.Phe234=
c.702C>T · rs147917851 · VCV3250569
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.2%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.339 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.2 | GERP -4.7 |
| Overall | ||
| CADD | 6.795 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.2%
East Asian · 36/18,030 alleles
Filtering AF
0.148%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.13%
Overall
0.0981%
1,265/1,289,744 alleles · rare
exomes 1,164/1,137,358 · genomes 101/152,386 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.2% | 501 |
| European (non-Finnish) | 0.114% | 876 |
| Admixed American | 0.0666% | 1,503 |
| Remaining individualsnot grpmax-eligible | 0.0527% | 1,897 |
| South Asian | 0.0358% | 2,794 |
| African / African-American | 0.0212% | 4,715 |
| Finnishnot grpmax-eligible | 0.0211% | 4,739 |
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
- ZNF142
- Protein
- p.Phe234=
- Coding
- c.702C>T
- MANE Select
- NM_001379659
- dbSNP
- rs147917851
- Type
- single nucleotide variant
- Location
- chr2:218651879 (GRCh38)
- Gene constraint
- LOEUF 0.832 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.51
Similar variants
- ZNF142 p.Arg1259Ter Pathogenic/Likely pathogenic ★★ same type
- ZNF142 p.Arg1544Ter Pathogenic ★★ same type
- ZNF142 p.Arg618Ter Pathogenic ★★ same type
- ZNF142 p.Arg677Ter Pathogenic/Likely pathogenic ★★ same type
- ZNF142 p.Arg836Ter Pathogenic ★★ same type
- ZNF142 p.Gln1372Ter Pathogenic/Likely pathogenic ★★ same type
- ZNF142 p.Ala1790Thr Uncertain significance ★★ ⚠ same type
- ZNF142 p.Ala478Val 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/znf142-p-phe234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown