POF1B p.Ser533=
c.1599C>A · VCV4951839
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0256%, 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 1.8 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 6.845 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0256%
Middle Eastern · 1/3,908 alleles
Filtering AF
0.00059%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000221%
Overall
0.00042%
5/1,189,803 alleles · ultra-rare
exomes 5/1,079,147 · genomes 0/110,656 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0256% | 3,908 |
| African / African-American | 0.00356% | 28,119 |
| Admixed American | 0.00222% | 45,132 |
| Remaining individualsnot grpmax-eligible | 0.00214% | 46,818 |
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
- POF1B
- Protein
- p.Ser533=
- Coding
- c.1599C>A
- MANE Select
- NM_024921
- Type
- single nucleotide variant
- Location
- chrX:85303456 (GRCh38)
- Structure
- AlphaFold pLDDT 62.59 · 1 PDB
Similar variants
- POF1B p.Ser533Pro Uncertain significance ★ ⚠ same residue
- POF1B p.Arg468= Uncertain significance ★★ same type
- POF1B p.Met320Ile Uncertain significance ★★ ⚠ same type
- POF1B c.1566+10G>A Benign ★★ same type
- POF1B c.1764+3A>G Benign ★★ same type
- POF1B c.*1019C>A Benign ★★ same type
- POF1B c.*268T>G Benign ★★ same type
- POF1B c.*312A>C Benign ★★ 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/pof1b-p-ser533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown