POMP c.101+2T>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.88 | loss · gain 0.13 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.6, phastCons 1 |
| Non-coding constraint | Z 1.01 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 28.6 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- POMP
- Coding
- c.101+2T>C
- MANE Select
- NM_015932
- Type
- single nucleotide variant
- Location
- chr13:28662509 (GRCh38)
- Gene constraint
- LOEUF 1.191 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 81.76 · 11 PDB
Similar variants
- POMP p.Arg32Gln Uncertain significance ★★ ⚠ same type
- POMP p.Arg32Trp Uncertain significance ★★ ⚠ same type
- POMP p.Asn108His Uncertain significance ★★ ⚠ same type
- POMP p.Asn40Ser Uncertain significance ★★ ⚠ same type
- POMP p.Gln56His Uncertain significance ★★ ⚠ same type
- POMP p.His28Pro Uncertain significance ★★ ⚠ same type
- POMP p.Ile112Val Uncertain significance ★★ ⚠ same type
- POMP p.Leu30Phe 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/pomp-c-101-plus-2t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown