SLX4 p.Phe655=
c.1965T>C · rs2151129331 · VCV1692004
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Fanconi anemia
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 4.3 | GERP 0.48, phastCons 1 |
| Overall | ||
| CADD | 7.476 | PHRED · no single calibrated threshold — expert panels disagree |
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
- SLX4
- Protein
- p.Phe655=
- Coding
- c.1965T>C
- MANE Select
- NM_032444
- dbSNP
- rs2151129331
- Type
- single nucleotide variant
- Location
- chr16:3595653 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 47.20 · 7 PDB
- Residue 655
- the 'interaction with slx4ip, ercc4/xpf and msh2' region
Disease context
Fanconi anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hereditary isolated aplastic anemia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Childhood
Similar variants
- SLX4 p.Phe655Ser Uncertain significance ★ ⚠ same residue
- SLX4 c.1684-1G>A Likely pathogenic ★★ same condition
- SLX4 p.Arg1666Ter Pathogenic/Likely pathogenic ★★ same condition
- SLX4 p.Arg481Ter Pathogenic/Likely pathogenic ★★ same condition
- SLX4 p.Arg713Ter Pathogenic/Likely pathogenic ★★ same condition
- SLX4 p.Gln1201Ter Pathogenic/Likely pathogenic ★★ same condition
- SLX4 p.Gln1306Ter Pathogenic ★★ same condition
- SLX4 p.Gln1386Ter 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/slx4-p-phe655 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown