ANKZF1 p.Ser128=
c.384G>A · rs372550492 · VCV1416637
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, 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 -0.41 | GERP -4.7 |
| Overall | ||
| CADD | 5.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,898 alleles
Filtering AF
0.000615%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000474%
Overall
0.000929%
15/1,614,022 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00134% | 74,898 |
| European (non-Finnish) | 0.0011% | 90,770 |
| South Asian | 0.0011% | 91,088 |
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.Ser128=
- Coding
- c.384G>A
- MANE Select
- NM_018089
- dbSNP
- rs372550492
- Type
- single nucleotide variant
- Location
- chr2:219232509 (GRCh38)
- Gene constraint
- LOEUF 1.125 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.09
- Residue 128
- the 'disordered' region
Similar variants
- ANKZF1 p.Ser128Leu Uncertain significance ★ ⚠ same residue
- ANKZF1 p.Ser128Ter 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
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-ser128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown