ANLN p.Ser339=
c.1017C>T · rs532120296 · VCV744018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00814%, nfe)
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 -0.22 | GERP 0.62, phastCons 0.001 |
| Overall | ||
| CADD | 6.773 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00814%
European (non-Finnish) · 96/1,179,852 alleles
Filtering AF
0.00681%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.00613%
99/1,613,712 alleles · very rare
exomes 90/1,461,590 · genomes 9/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00814% | 12,290 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,823 |
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
- ANLN
- Protein
- p.Ser339=
- Coding
- c.1017C>T
- MANE Select
- NM_018685
- dbSNP
- rs532120296
- Type
- single nucleotide variant
- Location
- chr7:36407877 (GRCh38)
- Gene constraint
- LOEUF 0.537 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 60.09 · 3 PDB
- Residue 339
- a modified residue (phosphoserine); the 'interaction with f-actin' region
Similar variants
- ANLN p.Arg431Cys Pathogenic/Likely pathogenic ★★ same type
- ANLN c.2653-13G>A Uncertain significance ★★ same type
- ANLN p.Ala47Gly Uncertain significance ★★ ⚠ same type
- ANLN p.Ala828Thr Uncertain significance ★★ ⚠ same type
- ANLN p.Ala940Thr Uncertain significance ★★ ⚠ same type
- ANLN p.Arg1040His Uncertain significance ★★ ⚠ same type
- ANLN p.Arg154Cys Uncertain significance ★★ ⚠ same type
- ANLN p.Arg376Cys 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/anln-p-ser339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown