POP1 p.Ile400=
c.1200C>T · rs577149443 · VCV2957186
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, 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 -8.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.427 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,058 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000901%
Overall
0.00167%
27/1,612,364 alleles · very rare
exomes 25/1,460,126 · genomes 2/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,765 |
| East Asian | 0.00223% | 44,866 |
| European (non-Finnish) | 0.0017% | 58,923 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,446 |
| African / African-American | 0.00133% | 74,970 |
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
- POP1
- Protein
- p.Ile400=
- Coding
- c.1200C>T
- MANE Select
- NM_001145860
- dbSNP
- rs577149443
- Type
- single nucleotide variant
- Location
- chr8:98136670 (GRCh38)
- Structure
- AlphaFold pLDDT 76.08
Similar variants
- POP1 p.Gln778Ter Pathogenic/Likely pathogenic ★★ same type
- POP1 p.Val696Asp Likely pathogenic ★★ ⚠ same type
- POPDC1 p.Arg88Ter Pathogenic/Likely pathogenic ★★ same type
- POPDC1 p.Ser201Phe Likely pathogenic ★★ same type
- POP1 p.Ala1011Thr Uncertain significance ★★ ⚠ same type
- POP1 p.Ala166Pro Uncertain significance ★★ ⚠ same type
- POP1 p.Ala44Pro Uncertain significance ★★ ⚠ same type
- POP1 p.Ala497Val 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/pop1-p-ile400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown