DNASE1L3 p.Pro142=
c.426C>T · rs988376336 · VCV1923190
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00203%, nfe)
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 -0.069 | GERP -3.7 |
| Overall | ||
| CADD | 0.616 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00203%
European (non-Finnish) · 24/1,179,960 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00116%
Overall
0.00161%
26/1,613,926 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00203% | 49,165 |
| Admixed American | 0.00167% | 60,000 |
| African / African-American | 0.00134% | 74,904 |
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
- DNASE1L3
- Protein
- p.Pro142=
- Coding
- c.426C>T
- MANE Select
- NM_004944
- dbSNP
- rs988376336
- Type
- single nucleotide variant
- Location
- chr3:58204776 (GRCh38)
- Gene constraint
- LOEUF 1.122 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.08 · 1 PDB
Similar variants
- DNASE1L3 p.Pro142Thr Uncertain significance ★★ ⚠ same residue
- DNASE1L3 p.Pro142Ala Uncertain significance ★ ⚠ same residue
- DNASE1L3 c.802-20C>G Uncertain significance ★★ same type
- DNASE1L3 p.Ala18Thr Uncertain significance ★★ ⚠ same type
- DNASE1L3 p.Ala201Thr Uncertain significance ★★ ⚠ same type
- DNASE1L3 p.Ala268Gly Uncertain significance ★★ ⚠ same type
- DNASE1L3 p.Arg22Lys Uncertain significance ★★ ⚠ same type
- DNASE1L3 p.Arg285Lys 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/dnase1l3-p-pro142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown