INTS6 p.Pro43fs
c.128del · VCV4529716
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 18 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.29 | GERP -2.5, phastCons 0.002 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- INTS6
- Protein
- p.Pro43fs
- Coding
- c.128del
- MANE Select
- NM_012141
- Type
- Deletion
- Location
- chr13:51452039 (GRCh38)
- Gene constraint
- LOEUF 0.23 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 72.80 · 9 PDB
- Residue 43
- the vwfa domain; an α-helix
Similar variants
- SERPINE3 p.Ala43Thr Uncertain significance ★ ⚠ same residue
- INTS6 p.Ala544_Tyr545insTer Pathogenic ★ same type
- INTS6 p.Val278fs Likely pathogenic ★ same type
- INTS6 p.Pro323fs Uncertain significance ★ same type
- INTS6 p.Tyr497fs Uncertain significance ★ same type
- INTS6 c.613+3_613+6del Pathogenic 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/ints6-p-pro43fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown