YIPF5 p.Cys244=
c.732C>T · VCV3818013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.6 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 12.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,854 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00167%
27/1,614,016 alleles · very rare
exomes 23/1,461,802 · genomes 4/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,214 |
| Admixed American | 0.00667% | 15,004 |
| South Asian | 0.00329% | 30,357 |
| European (non-Finnish) | 0.00136% | 73,749 |
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
- YIPF5
- Protein
- p.Cys244=
- Coding
- c.732C>T
- MANE Select
- NM_030799
- Type
- single nucleotide variant
- Location
- chr5:144160439 (GRCh38)
- Gene constraint
- LOEUF 0.464 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 66.45
Similar variants
- YIPF5 p.Val51Ile Uncertain significance ★★ ⚠ same type
- YIPF5 p.Ala198Thr Uncertain significance ★ ⚠ same type
- YIPF5 p.Ala245Thr Uncertain significance ★ ⚠ same type
- YIPF5 p.Asp20Gly Uncertain significance ★ ⚠ same type
- YIPF5 p.Asp43Asn Uncertain significance ★ ⚠ same type
- YIPF5 p.Asp43Val Uncertain significance ★ ⚠ same type
- YIPF5 p.Cys179Phe Uncertain significance ★ ⚠ same type
- YIPF5 p.Gln21Arg 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/yipf5-p-cys244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown