DZIP1 p.Thr222=
c.666T>G · rs35961322 · VCV781123
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.99%, 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 0.25 | GERP 1.4, phastCons 0.4 |
| Overall | ||
| CADD | 2.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.99%
African / African-American · 3,746/75,050 alleles
Filtering AF
4.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.8%
Overall
0.278%
4,484/1,614,116 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.99% | 20 |
| Remaining individualsnot grpmax-eligible | 0.408% | 245 |
| Middle Eastern | 0.363% | 276 |
| Admixed American | 0.35% | 286 |
| Ashkenazi Jewishnot grpmax-eligible | 0.182% | 548 |
| South Asian | 0.0176% | 5,692 |
| European (non-Finnish) | 0.0153% | 6,519 |
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
- DZIP1
- Protein
- p.Thr222=
- Coding
- c.666T>G
- MANE Select
- NM_198968
- dbSNP
- rs35961322
- Type
- single nucleotide variant
- Location
- chr13:95633253 (GRCh38)
- Gene constraint
- LOEUF 1.01 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.55
- Residue 222
- the 'mediates interaction with gli3 and localization to the cilium basal body' region; the 'required for interaction with daz1' region
Similar variants
- DZIP1 p.Thr222Ala Uncertain significance ★ ⚠ same residue
- DZIP1 p.His262Arg Uncertain significance ★★ ⚠ same type
- DZIP1 p.Met664Leu Benign ★★ same type
- DZIP1 p.Ala124Val Uncertain significance ★ ⚠ same type
- DZIP1 p.Ala211Ser Uncertain significance ★ ⚠ same type
- DZIP1 p.Ala265Gly Uncertain significance ★ ⚠ same type
- DZIP1 p.Ala32Val Uncertain significance ★ ⚠ same type
- DZIP1 p.Ala380Gly 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/dzip1-p-thr222 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown