FANCD2 p.Ser8Ter
c.23C>A · VCV3588138
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Fanconi anemia complementation group D2
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 44 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 34.0 | 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
- FANCD2
- Protein
- p.Ser8Ter
- Coding
- c.23C>A
- MANE Select
- NM_001018115
- Type
- single nucleotide variant
- Location
- chr3:10028680 (GRCh38)
- Gene constraint
- LOEUF 0.777 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 77.24 · 13 PDB
- Residue 8
- the 'interaction with fance' region; the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- FANCD2 c.1279-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FANCD2 c.1279-2A>G Likely pathogenic ★★ same condition
- FANCD2 c.1948-16T>G Pathogenic ★★ same condition
- FANCD2 c.1948-6C>A Pathogenic/Likely pathogenic ★★ same condition
- FANCD2 c.206-1G>T Likely pathogenic ★★ same condition
- FANCD2 c.2169-1G>C Likely pathogenic ★★ same condition
- FANCD2 c.2269+1G>A Likely pathogenic ★★ same condition
- FANCD2 c.2715+1G>A Pathogenic/Likely pathogenic ★★ same condition
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/fancd2-p-ser8ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown