GPC4 p.Phe108=
c.324C>T · rs779109574 · VCV721968
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.249%, sas)
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 3 | GERP 0.79, phastCons 1 |
| Overall | ||
| CADD | 8.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
South Asian · 41/16,442 alleles
Filtering AF
0.189%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.168%
Overall
0.0813%
533/655,240 alleles · rare
exomes 521/596,879 · genomes 12/58,361 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.249% | 401 |
| Admixed American | 0.208% | 480 |
| Ashkenazi Jewishnot grpmax-eligible | 0.129% | 772 |
| Remaining individualsnot grpmax-eligible | 0.101% | 986 |
| Finnishnot grpmax-eligible | 0.0767% | 1,303 |
| European (non-Finnish) | 0.0728% | 1,373 |
| Middle Eastern | 0.0617% | 1,622 |
| East Asian | 0.0568% | 1,761 |
| African / African-American | 0.0442% | 2,260 |
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
- GPC4
- Protein
- p.Phe108=
- Coding
- c.324C>T
- MANE Select
- NM_001448
- dbSNP
- rs779109574
- Type
- single nucleotide variant
- Location
- chrX:133324532 (GRCh38)
- Structure
- AlphaFold pLDDT 83.68
Similar variants
- GPC4 p.Gln506Ter Pathogenic ★★ same type
- GPC4 p.Ala217Val Uncertain significance ★★ ⚠ same type
- GPC4 p.Arg219His Uncertain significance ★★ ⚠ same type
- GPC4 p.Asn514Ser Uncertain significance ★★ ⚠ same type
- GPC4 p.Asn92Ser Uncertain significance ★★ ⚠ same type
- GPC4 p.Lys26Glu Uncertain significance ★★ ⚠ same type
- GPC4 p.Pro343Leu Uncertain significance ★★ ⚠ same type
- GPC4 c.160+96A>G 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/gpc4-p-phe108 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown