ATL1 p.Ser10=
c.30T>C · rs146613929 · VCV471249
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.236%, afr)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>G here scores Δ0.92 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.3 | GERP -4.9 |
| Overall | ||
| CADD | 10.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.236%
African / African-American · 177/74,968 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.197%
Overall
0.0136%
220/1,613,762 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.236% | 424 |
| Admixed American | 0.045% | 2,222 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,943 |
| European (non-Finnish) | 0.000509% | 196,636 |
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
- ATL1
- Protein
- p.Ser10=
- Coding
- c.30T>C
- MANE Select
- NM_015915
- dbSNP
- rs146613929
- Type
- single nucleotide variant
- Location
- chr14:50560295 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.36 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 14 PDB
- Residue 10
- a modified residue (phosphoserine); the 'n-terminal hypervariable region (hvr)' region; the 'disordered' region
Similar variants
- ATL1 p.Arg217Gln Pathogenic/Likely pathogenic ★★ same condition
- ATL1 p.Arg239Cys Pathogenic/Likely pathogenic ★★ same condition
- ATL1 p.Arg239His Likely pathogenic ★★ same condition
- ATL1 p.Arg403Pro Likely pathogenic ★★ same condition
- ATL1 p.Arg415Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ATL1 p.Arg416Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ATL1 p.Arg495Trp Pathogenic/Likely pathogenic ★★ same condition
- ATL1 p.Gly409Cys Pathogenic/Likely pathogenic ★★ 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/atl1-p-ser10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown