PROP1 p.Ser38=
c.114G>A · rs373656666 · VCV1140025
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -2 | |
| Overall | ||
| CADD | 2.152 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,014 alleles
Filtering AF
0.00166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00143%
Overall
0.00226%
36/1,593,168 alleles · ultra-rare
exomes 28/1,441,070 · genomes 8/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,014 |
| Admixed American | 0.00538% | 18,576 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,832 |
| European (non-Finnish) | 0.00239% | 41,757 |
| East Asian | 0.00227% | 44,066 |
| African / African-American | 0.00134% | 74,552 |
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
- PROP1
- Protein
- p.Ser38=
- Coding
- c.114G>A
- MANE Select
- NM_006261
- dbSNP
- rs373656666
- Type
- single nucleotide variant
- Location
- chr5:177994334 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI 0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.74
- Residue 38
- the 'disordered' region
Similar variants
- PROP1 p.Ser38Leu Uncertain significance ★ ⚠ same residue
- PROP1 p.Ser38fs Likely pathogenic ★ same residue
- PROP1 c.109+1G>A Pathogenic ★★ same type
- PROP1 c.110-2A>G Likely pathogenic ★★ same type
- PROP1 c.343-1G>A Likely pathogenic ★★ same type
- PROP1 p.Arg112Ter Pathogenic/Likely pathogenic ★★ same type
- PROP1 p.Arg120Cys Pathogenic/Likely pathogenic ★★ same type
- PROP1 p.Arg125Gln Likely 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/prop1-p-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown