ANK3 p.Ser4037=
c.12111G>A · rs557280144 · VCV3067460
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0439%, sas)
Conditions
1
Inborn genetic diseases
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 |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP 5.3, phastCons 1 |
| Overall | ||
| CADD | 13.94 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0439%
South Asian · 40/91,080 alleles
Filtering AF
0.0331%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.00595%
96/1,614,190 alleles · ultra-rare
exomes 88/1,461,866 · genomes 8/152,324 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0439% | 2,277 |
| East Asian | 0.0357% | 2,805 |
| African / African-American | 0.004% | 25,020 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
| Finnishnot grpmax-eligible | 0.00312% | 32,023 |
| European (non-Finnish) | 0.00263% | 38,065 |
| Admixed American | 0.00167% | 60,024 |
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
- ANK3
- Protein
- p.Ser4037=
- Coding
- c.12111G>A
- MANE Select
- NM_020987
- dbSNP
- rs557280144
- Type
- single nucleotide variant
- Location
- chr10:60068770 (GRCh38)
- Gene constraint
- LOEUF 0.16 · pLI 1.00 (gnomAD)
- Residue 4037
- the 'disordered' region
Similar variants
- ANK3 p.Ala1534Val Uncertain significance ★★ same condition
- ANK3 p.Ala218Thr Uncertain significance ★★ same condition
- ANK3 p.Ala259Thr Uncertain significance ★★ same condition
- ANK3 p.Ala324Gly Uncertain significance ★★ ⚠ same condition
- ANK3 p.Ala3262Val Uncertain significance ★★ ⚠ same condition
- ANK3 p.Ala540Thr Uncertain significance ★★ same condition
- ANK3 p.Arg1012Cys Uncertain significance ★★ same condition
- ANK3 p.Arg1623Gln Uncertain significance ★★ same condition
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/ank3-p-ser4037 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown