DZIP1L p.Ala520=
c.1560G>T · VCV3356550
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00271%, nfe)
Conditions
1
DZIP1L-related disorder
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 0.56 | GERP -1.1, phastCons 0.63 |
| Overall | ||
| CADD | 7.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00271%
European (non-Finnish) · 32/1,180,030 alleles
Filtering AF
0.00196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00168%
Overall
0.00198%
32/1,614,098 alleles · very rare
exomes 31/1,461,868 · genomes 1/152,230 · joint denominator
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
- DZIP1L
- Protein
- p.Ala520=
- Coding
- c.1560G>T
- MANE Select
- NM_173543
- Type
- single nucleotide variant
- Location
- chr3:138071698 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.03
- Residue 520
- a UniProt-annotated variant site (in pkd5); the 'disordered' region
Disease context
DZIP1L-related disorder
Similar variants
- DZIP1L p.Ala520Thr Uncertain significance ★ ⚠ same residue
- DZIP1L p.Arg574His Uncertain significance ⚠ same condition
- DZIP1L p.Glu194Gln Uncertain significance ⚠ same condition
- DZIP1L c.1063-5G>T Likely benign same condition
- DZIP1L p.Leu115= Likely benign same condition
- DZIP1L p.Lys680= Likely benign same condition
- DZIP1L p.Pro699= Likely benign same condition
- DZIP1L p.Ser617Phe 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/dzip1l-p-ala520 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown