POMP p.Leu141=
c.423G>A · rs374938538 · VCV3013883
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 5.8 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 5.264 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,078 alleles
Filtering AF
0.000543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000429%
Overall
0.000806%
13/1,613,374 alleles · very rare
exomes 12/1,461,174 · genomes 1/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,078 |
| European (non-Finnish) | 0.00102% | 98,287 |
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.Leu141=
- Coding
- c.423G>A
- MANE Select
- NM_015932
- dbSNP
- rs374938538
- Type
- single nucleotide variant
- Location
- chr13:28678099 (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-p-leu141 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown