POMP p.Arg106=
c.318G>A · rs758881701 · VCV1634388
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00085%, nfe)
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 1.5 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 8.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00085%
European (non-Finnish) · 10/1,176,032 alleles
Filtering AF
0.00043%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000314%
Overall
0.000621%
10/1,609,496 alleles · very rare
exomes 8/1,457,434 · genomes 2/152,062 · joint denominator
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
- POMP
- Protein
- p.Arg106=
- Coding
- c.318G>A
- MANE Select
- NM_015932
- dbSNP
- rs758881701
- Type
- single nucleotide variant
- Location
- chr13:28672392 (GRCh38)
- Gene constraint
- LOEUF 1.191 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 81.76 · 11 PDB
- Residue 106
- an α-helix
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-p-arg106 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown