DZIP1L p.Pro590=
c.1770C>T · rs6776890 · VCV1233666
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 21.1%, 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -3.4 |
| Overall | ||
| CADD | 0.336 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
21.1%
African / African-American · 15,696/74,270 alleles
Filtering AF
20.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 20.7%
Overall
2.04%
32,505/1,591,422 alleles · common
exomes 22,173/1,439,344 · genomes 10,332/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 21.1% | 5 |
| Admixed American | 2.48% | 40 |
| Remaining individualsnot grpmax-eligible | 2.43% | 41 |
| Middle Eastern | 2.22% | 45 |
| Finnishnot grpmax-eligible | 1.42% | 70 |
| European (non-Finnish) | 1.07% | 94 |
| Ashkenazi Jewishnot grpmax-eligible | 0.4% | 250 |
| East Asian | 0.289% | 345 |
| South Asian | 0.177% | 566 |
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.Pro590=
- Coding
- c.1770C>T
- MANE Select
- NM_173543
- dbSNP
- rs6776890
- Type
- single nucleotide variant
- Location
- chr3:138068213 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.03
- Residue 590
- a UniProt-annotated variant site (in pkd5); the 'disordered' region
Similar variants
- DZIP1L p.Pro590Ser Uncertain significance ★ ⚠ same residue
- DZIP1L p.Glu358Ter Pathogenic/Likely pathogenic ★★ same type
- DZIP1L p.Ala190Val Uncertain significance ★★ ⚠ same type
- DZIP1L p.Arg124Cys Uncertain significance ★★ ⚠ same type
- DZIP1L p.Arg131Cys Uncertain significance ★★ ⚠ same type
- DZIP1L p.Arg233Gln Uncertain significance ★★ ⚠ same type
- DZIP1L p.Arg37His Uncertain significance ★★ ⚠ same type
- DZIP1L p.Arg48Trp 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/dzip1l-p-pro590 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown