ATL1 p.Val100=
c.300T>G · rs863224772 · VCV216696
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 0.66, phastCons 1 |
| Overall | ||
| CADD | 13.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,936 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000744%
12/1,613,824 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,936 |
| European (non-Finnish) | 0.000932% | 107,266 |
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.Val100=
- Coding
- c.300T>G
- MANE Select
- NM_015915
- dbSNP
- rs863224772
- Type
- single nucleotide variant
- Location
- chr14:50590958 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.36 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 14 PDB
- Residue 100
- the gb1/rhd3-type g domain; a turn
Similar variants
- ATL1 p.Val100Phe Uncertain significance ★ ⚠ same residue
- ATL1 p.Val100Ala Uncertain significance ★ ⚠ same residue
- 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
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-val100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown