IMPDH1 p.Pro7Ser
c.19C>T · rs1799031509 · VCV866094
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00045%, nfe)
Conditions
1
IMPDH1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.058 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.47 | GERP -2, phastCons 0.003 |
| Regional constraint | o/e 1.00 | unconstrained · MANE · 6,191 bp · p 0.96 · regional, not allelic |
| Overall | ||
| CADD | 9.964 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00045%
European (non-Finnish) · 5/1,111,132 alleles
Filtering AF
0.000132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.6e-05%
Overall
0.000342%
5/1,460,512 alleles · very rare
exomes 5/1,308,224 · genomes 0/152,288 · 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
- IMPDH1
- Protein
- p.Pro7Ser
- Coding
- c.19C>T
- MANE Select
- NM_000883
- dbSNP
- rs1799031509
- Type
- single nucleotide variant
- Location
- chr7:128409883 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.71 · 18 PDB
Disease context
IMPDH1-related disorder
Similar variants
- IMPDH1 p.Pro7= Likely benign ★ same residue
- IMPDH1 p.Arg309Pro Pathogenic/Likely pathogenic ★★ same condition
- IMPDH1 p.Asp311Asn Pathogenic/Likely pathogenic ★★ same condition
- IMPDH1 p.Asp311Gly Pathogenic/Likely pathogenic ★★ same condition
- IMPDH1 p.Gly241Ser Uncertain significance ★★ same condition
- IMPDH1 p.Asn315Lys Likely pathogenic ★ same condition
- IMPDH1 p.Asp311Ala Likely pathogenic ★ same condition
- IMPDH1 p.Asp311Glu Likely pathogenic ★ same condition
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/impdh1-p-pro7ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown