POMC p.Val78=
c.234C>A · rs1173071382 · VCV3001694
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000348%, 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 11 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 14.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000348%
European (non-Finnish) · 4/1,150,880 alleles
Filtering AF
8.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.5e-05%
Overall
0.000257%
4/1,556,640 alleles · very rare
exomes 3/1,404,436 · genomes 1/152,204 · 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
- POMC
- Protein
- p.Val78=
- Coding
- c.234C>A
- MANE Select
- NM_000939
- dbSNP
- rs1173071382
- Type
- single nucleotide variant
- Location
- chr2:25161651 (GRCh38)
- Gene constraint
- LOEUF 1.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.47 · 13 PDB
Similar variants
- POMC c.-11C>A Pathogenic ★★ same type
- POMC p.Ala164Val Uncertain significance ★★ ⚠ same type
- POMC p.Ala213Val Uncertain significance ★★ ⚠ same type
- POMC p.Arg145Cys Uncertain significance ★★ ⚠ same type
- POMC p.Arg145His Uncertain significance ★★ ⚠ same type
- POMC p.Arg25Cys Uncertain significance ★★ ⚠ same type
- POMC p.Glu167Ter Uncertain significance ★★ same type
- POMC p.Glu206Ter 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/pomc-p-val78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown