ANKRD53 p.Ser403=
c.1209G>A · VCV3873834
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00245%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Pangolin | Δ0.61 | gain · loss 0.00 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -3.5 |
| Overall | ||
| CADD | 0.148 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00245%
East Asian · 1/40,886 alleles
Filtering AF
0.000395%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000148%
Overall
0.000193%
3/1,550,874 alleles · very rare
exomes 3/1,398,582 · genomes 0/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00245% | 40,886 |
| South Asian | 0.00238% | 42,029 |
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
- ANKRD53
- Protein
- p.Ser403=
- Coding
- c.1209G>A
- MANE Select
- NM_001115116
- Type
- single nucleotide variant
- Location
- chr2:70984916 (GRCh38)
- Gene constraint
- LOEUF 1.379 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.41
Similar variants
- ANKRD53 p.Ala11Glu Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala143Asp Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala148Thr Uncertain significance ★ same type
- ANKRD53 p.Ala219Ser Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala242Thr Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala310Thr Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala39Pro Uncertain significance ★ ⚠ same type
- ANKRD53 p.Ala434Pro 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/ankrd53-p-ser403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown