LTN1 p.Ser511=
c.1533C>T · rs149033003 · VCV2652579
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0986%, mid)
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 -0.028 | GERP -3.5 |
| Overall | ||
| CADD | 7.427 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0986%
Middle Eastern · 6/6,084 alleles
Filtering AF
0.0429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0293%
Overall
0.00304%
49/1,613,628 alleles · ultra-rare
exomes 38/1,461,694 · genomes 11/151,934 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0986% | 1,014 |
| African / African-American | 0.0254% | 3,936 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
| East Asian | 0.00223% | 44,890 |
| South Asian | 0.0022% | 45,522 |
| Admixed American | 0.00167% | 59,916 |
| European (non-Finnish) | 0.00144% | 69,411 |
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
- LTN1
- Protein
- p.Ser511=
- Coding
- c.1533C>T
- MANE Select
- NM_015565
- dbSNP
- rs149033003
- Type
- single nucleotide variant
- Location
- chr21:28966958 (GRCh38)
- Gene constraint
- LOEUF 0.471 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 80.79 · 2 PDB
- Residue 511
- an α-helix
Similar variants
- LTN1 p.Ala500Val Benign ★★ same type
- LTN1 p.Glu462Asp Benign ★★ same type
- LTN1 c.64G>A Uncertain significance ★ same type
- LTN1 c.-15G>T Uncertain significance ★ same type
- LTN1 c.-26C>T Uncertain significance ★ same type
- LTN1 c.-30A>G Uncertain significance ★ same type
- LTN1 c.-35G>A Uncertain significance ★ same type
- LTN1 c.-9A>G 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/ltn1-p-ser511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown