DIS3L2 c.52+9del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
Perlman syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.03 | GERP -0.24, phastCons 0.002 |
| Non-coding constraint | Z 3.36 | 1 kb window · o/e 0.77 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- DIS3L2
- Coding
- c.52+9del
- MANE Select
- NM_152383
- dbSNP
- rs2106220830
- Type
- Deletion
- Location
- chr2:232014985 (GRCh38)
- Gene constraint
- LOEUF 0.468 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 83.26 · 4 PDB
Similar variants
- DIS3L2 p.Arg17fs Pathogenic/Likely pathogenic ★★ same condition
- DIS3L2 p.Asn740fs Pathogenic ★★ same condition
- DIS3L2 p.Cys216fs Pathogenic/Likely pathogenic ★★ same condition
- DIS3L2 p.Leu768fs Pathogenic/Likely pathogenic ★★ same condition
- DIS3L2 p.Thr662fs Pathogenic/Likely pathogenic ★★ same condition
- DIS3L2 p.Lys870del Uncertain significance ★★ same condition
- DIS3L2 c.211-9del Likely benign ★★ same condition
- DIS3L2 c.602-19_602-16del Likely benign ★★ same condition
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/dis3l2-c-52-plus-9del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown