CCDC88A p.Gln537Ter
c.1609C>T · rs1247617743 · VCV2035839
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 14 of 33 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.29 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CCDC88A
- Protein
- p.Gln537Ter
- Coding
- c.1609C>T
- MANE Select
- NM_001365480
- dbSNP
- rs1247617743
- Type
- single nucleotide variant
- Location
- chr2:55336728 (GRCh38)
- Gene constraint
- LOEUF 0.25 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.09 · 1 PDB
Similar variants
- CCDC88A p.Ala1536Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala155Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala158Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala1770Val Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala194Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala72Thr Uncertain significance ★★ ⚠ same type
- CCDC88A p.Ala845Gly Uncertain significance ★★ ⚠ same type
- CCDC88A p.Arg1169His 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/ccdc88a-p-gln537ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown