LINS1 p.Asp636=
c.1908C>T · rs753046177 · VCV435756
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.029%, eas)
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 -0.35 | GERP -5, phastCons 0.001 |
| Overall | ||
| CADD | 4.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.029%
East Asian · 13/44,874 alleles
Filtering AF
0.0171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.00167%
27/1,613,530 alleles · ultra-rare
exomes 20/1,461,252 · genomes 7/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.029% | 3,452 |
| African / African-American | 0.00533% | 18,751 |
| South Asian | 0.0011% | 91,048 |
| European (non-Finnish) | 0.000763% | 131,059 |
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
- LINS1
- Protein
- p.Asp636=
- Coding
- c.1908C>T
- MANE Select
- NM_001040616
- dbSNP
- rs753046177
- Type
- single nucleotide variant
- Location
- chr15:100569604 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- LINS1 p.Leu393Ter Pathogenic/Likely pathogenic ★★ same type
- LINS1 c.1394+4A>G Uncertain significance ★★ same type
- LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same type
- LINS1 p.Asn433Ser Uncertain significance ★★ ⚠ same type
- LINS1 p.Asp221Asn Uncertain significance ★★ ⚠ same type
- LINS1 p.Asp630Asn Uncertain significance ★★ ⚠ same type
- LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ same type
- LINS1 p.Leu757Ter 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/lins1-p-asp636 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown