Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 5.9 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 9.477 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,032 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,050 alleles · very rare
exomes 1/1,461,824 · genomes 1/152,226 · joint denominator
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
- PLCD1
- Protein
- p.Ile550=
- Coding
- c.1650C>T
- MANE Select
- NM_006225
- dbSNP
- rs1050868
- Type
- single nucleotide variant
- Location
- chr3:38009115 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.31
- Residue 550
- the pi-plc y-box domain
Similar variants
- PLCD1 p.Arg530Ter Pathogenic/Likely pathogenic ★★ same type
- PLCD1 p.Arg138His Uncertain significance ★★ ⚠ same type
- PLCD1 p.Arg476His Uncertain significance ★★ ⚠ same type
- PLCD1 p.Arg60Gln Uncertain significance ★★ ⚠ same type
- PLCD1 p.Pro417Arg Uncertain significance ★★ ⚠ same type
- PLCD1 p.Ser650Ala Uncertain significance ★★ ⚠ same type
- PLCD1 c.1607-42C>T Benign ★★ same type
- PLCD1 c.1724-186C>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/plcd1-p-ile550 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown