LINS1 p.His329=
c.987T>C · rs192389870 · VCV747496
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.065%, amr)
Conditions
1
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 0.51 | GERP -3.2, phastCons 0.021 |
| Overall | ||
| CADD | 0.485 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.065%
Admixed American · 39/60,026 alleles
Filtering AF
0.0488%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0432%
Overall
0.00335%
54/1,614,248 alleles · ultra-rare
exomes 29/1,461,884 · genomes 25/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.065% | 1,539 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,683 |
| African / African-American | 0.00266% | 37,538 |
| South Asian | 0.0011% | 91,090 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
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.His329=
- Coding
- c.987T>C
- MANE Select
- NM_001040616
- dbSNP
- rs192389870
- Type
- single nucleotide variant
- Location
- chr15:100573886 (GRCh38)
- Gene constraint
- LOEUF 0.867 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Similar variants
- LINS1 c.1394+4A>G Uncertain significance ★★ same condition
- LINS1 p.Ala338Val Uncertain significance ★★ ⚠ same condition
- LINS1 p.Asn433Ser Uncertain significance ★★ ⚠ same condition
- LINS1 p.Asp630Asn Uncertain significance ★★ ⚠ same condition
- LINS1 p.Ile494Thr Uncertain significance ★★ ⚠ same condition
- LINS1 p.Leu757Ter Uncertain significance ★★ same condition
- LINS1 p.Met449Ile Uncertain significance ★★ ⚠ same condition
- LINS1 p.Ala331Val Benign ★★ 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/lins1-p-his329 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown