PSIP1 p.Arg3=
c.9C>G · rs767069695 · VCV744702
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0285%, afr)
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 2.4 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0285%
African / African-American · 21/73,694 alleles
Filtering AF
0.0191%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.00318%
51/1,604,632 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0285% | 3,509 |
| Admixed American | 0.0219% | 4,557 |
| Middle Eastern | 0.017% | 5,896 |
| Remaining individualsnot grpmax-eligible | 0.00483% | 20,688 |
| South Asian | 0.00111% | 89,924 |
| European (non-Finnish) | 0.00102% | 97,982 |
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
- PSIP1
- Protein
- p.Arg3=
- Coding
- c.9C>G
- MANE Select
- NM_033222
- dbSNP
- rs767069695
- Type
- single nucleotide variant
- Location
- chr9:15510180 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.32 · 40 PDB
- Residue 3
- the pwwp domain; an α-helix
Similar variants
- PSIP1 c.72+8A>G Benign ★★ same type
- PSIP1 p.Gln472Leu Benign ★★ same type
- PSIP1 p.Leu478Val Benign ★★ same type
- PSIP1 p.Ala185Val Uncertain significance ★ ⚠ same type
- PSIP1 p.Ala265Pro Uncertain significance ★ ⚠ same type
- PSIP1 p.Ala32Asp Uncertain significance ★ ⚠ same type
- PSIP1 p.Ala453Thr Uncertain significance ★ ⚠ same type
- PSIP1 p.Arg354Trp 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/psip1-p-arg3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown