DZIP1L p.Arg45=
c.135C>T · rs141620783 · VCV2888989
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0813%, 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 -11 | GERP -3.8 |
| Overall | ||
| CADD | 0.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0813%
African / African-American · 61/75,076 alleles
Filtering AF
0.0648%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.059%
Overall
0.00502%
81/1,614,170 alleles · ultra-rare
exomes 45/1,461,782 · genomes 36/152,388 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0813% | 1,231 |
| South Asian | 0.00439% | 22,772 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| European (non-Finnish) | 0.00119% | 84,290 |
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.Arg45=
- Coding
- c.135C>T
- MANE Select
- NM_173543
- dbSNP
- rs141620783
- Type
- single nucleotide variant
- Location
- chr3:138103837 (GRCh38)
- Gene constraint
- LOEUF 1.257 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.03
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-arg45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown