INTS11 p.Lys234=
c.702G>A · VCV4085415
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.84 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.83 | loss · gain 0.59 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 21.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,052 alleles
Overall
0.000124%
2/1,609,990 alleles · ultra-rare
exomes 2/1,457,676 · genomes 0/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,052 |
| East Asian | 0.00223% | 44,768 |
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
- INTS11
- Protein
- p.Lys234=
- Coding
- c.702G>A
- MANE Select
- NM_017871
- Type
- single nucleotide variant
- Location
- chr1:1314824 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.82 · 15 PDB
Similar variants
- INTS11 c.28+1406C>T Uncertain significance ★★ same type
- INTS11 p.Ala241Thr Uncertain significance ★★ ⚠ same type
- INTS11 p.Arg231Cys Uncertain significance ★★ ⚠ same type
- INTS11 p.Gln467His Uncertain significance ★★ ⚠ same type
- INTS11 p.Glu227Lys Uncertain significance ★★ same type
- INTS11 p.His157Arg Uncertain significance ★★ ⚠ same type
- INTS11 c.1607+18C>A Benign ★★ same type
- INTS11 p.Arg196= Benign ★★ 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/ints11-p-lys234 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown