ANKZF1 p.Ser694=
c.2082C>T · rs375125143 · VCV2192899
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, 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 0.2 | GERP -2.7, phastCons 0.95 |
| Overall | ||
| CADD | 6.812 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
African / African-American · 20/74,908 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0147%
Overall
0.00149%
24/1,613,984 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0267% | 3,745 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| European (non-Finnish) | 8.47e-05% | 1,180,032 |
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
- ANKZF1
- Protein
- p.Ser694=
- Coding
- c.2082C>T
- MANE Select
- NM_018089
- dbSNP
- rs375125143
- Type
- single nucleotide variant
- Location
- chr2:219236346 (GRCh38)
- Gene constraint
- LOEUF 1.125 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.09
Similar variants
- ANKZF1 p.Ser694Phe Uncertain significance ★★ ⚠ same residue
- ANKZF1 p.Ala251Asp Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala269Thr Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala287Val Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala327Thr Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala391Val Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala486Thr Uncertain significance ★★ ⚠ same type
- ANKZF1 p.Ala529Val 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/ankzf1-p-ser694 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown