ANLN p.Lys1024=
c.3072A>G · rs761609956 · VCV3023836
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0705%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.69 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.66, phastCons 0.99 |
| Overall | ||
| CADD | 6.964 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0705%
South Asian · 63/89,316 alleles
Filtering AF
0.0566%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0515%
Overall
0.00406%
65/1,601,556 alleles · ultra-rare
exomes 65/1,449,194 · genomes 0/152,362 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0705% | 1,418 |
| Remaining individualsnot grpmax-eligible | 0.00323% | 31,005 |
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.Lys1024=
- Coding
- c.3072A>G
- MANE Select
- NM_018685
- dbSNP
- rs761609956
- Type
- single nucleotide variant
- Location
- chr7:36443856 (GRCh38)
- Gene constraint
- LOEUF 0.537 · pLI 0.08 (gnomAD)
- Structure
- AlphaFold pLDDT 60.09 · 3 PDB
- Residue 1024
- the ph domain; the 'localization to the cleavage furrow' 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-lys1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown