ZNF142 p.Pro86=
c.258A>G · rs3731872 · VCV1288603
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 23.3%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.48 | GERP 0.38, phastCons 1 |
| Overall | ||
| CADD | 10.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
23.3%
African / African-American · 17,426/74,768 alleles
Filtering AF
23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.9%
Overall
4.61%
73,830/1,600,634 alleles · common
exomes 59,859/1,448,410 · genomes 13,971/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 23.3% | 4 |
| East Asian | 11.2% | 9 |
| Remaining individualsnot grpmax-eligible | 5.19% | 19 |
| South Asian | 4.28% | 23 |
| Middle Eastern | 3.95% | 25 |
| European (non-Finnish) | 3.35% | 30 |
| Ashkenazi Jewishnot grpmax-eligible | 3.3% | 30 |
| Admixed American | 3.29% | 30 |
| Finnishnot grpmax-eligible | 3.08% | 32 |
| Amishnot grpmax-eligible | 2.3% | 43 |
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.Pro86=
- Coding
- c.258A>G
- MANE Select
- NM_001379659
- dbSNP
- rs3731872
- Type
- single nucleotide variant
- Location
- chr2:218656172 (GRCh38)
- Gene constraint
- LOEUF 0.832 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.51
- Residue 86
- the 'disordered' region
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-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown