DZIP1L p.Ser601=
c.1803C>T · rs143711142 · VCV2067196
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.256%, afr)
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 0.85 | GERP -3.1 |
| Overall | ||
| CADD | 4.952 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.256%
African / African-American · 188/73,452 alleles
Filtering AF
0.226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.215%
Overall
0.0156%
243/1,559,780 alleles · rare
exomes 120/1,407,506 · genomes 123/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.256% | 391 |
| Remaining individualsnot grpmax-eligible | 0.0499% | 2,005 |
| Admixed American | 0.0335% | 2,989 |
| Middle Eastern | 0.0194% | 5,150 |
| South Asian | 0.0036% | 27,797 |
| European (non-Finnish) | 0.000261% | 383,564 |
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.Ser601=
- Coding
- c.1803C>T
- MANE Select
- NM_173543
- dbSNP
- rs143711142
- Type
- single nucleotide variant
- Location
- chr3:138068180 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.03
- Residue 601
- a UniProt-annotated variant site (in pkd5); the 'disordered' region
Similar variants
- 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
- DZIP1L p.Arg500Gln 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-ser601 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown