SLX1A
protein-codingSLX1 homolog A, structure-specific endonuclease subunit, the group of GIY-YIG endonuclease domain containing
Gene summary
This gene encodes a protein that is an important regulator of genome stability. The protein represents the catalytic subunit of the SLX1-SLX4 structure-specific endonuclease, which can resolve DNA secondary structures that are formed during repair and recombination processes. Two identical copies of this gene are located on the p arm of chromosome 16 due to a segmental duplication; this record represents the more centromeric copy. Alternative splicing results in multiple transcript variants. Read-through transcription also occurs between this gene and the downstream SULT1A3 (sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3) gene. [provided by RefSeq, Nov 2010]
- GIYD1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLX1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001014999.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 30 | 2 | 32 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 30 | 4 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001014999.1 | 6 | MANE Select | |
| Ensembl | ENSP00000251303.7 | 6 | MANE Select | |
| RefSeq | NP_001015000.1 | 5 | Standard | |
| Ensembl | ENSP00000333945.4 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Fanconi anemia pathway - Homo sapiens (human)
- HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
- Fanconi Anemia Pathway
- DNA Repair
- DNA Double-Strand Break Repair
Biological Process
- double-strand break repair via homologous recombination
- DNA repair
- DNA double-strand break processing involved in repair via single-strand annealing
- telomere maintenance via telomere lengthening
- interstrand cross-link repair
Molecular Function
- endodeoxyribonuclease activity
- protein binding
- crossover junction endodeoxyribonuclease activity
- 5'-flap endonuclease activity
- metal ion binding
Cellular Component
- nucleoplasm
- Slx1-Slx4 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000251303
- Coding exons
- 6
- Length
- 3675
- Individuals with no LoFs
- 120672
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 120674
- p
- 0.00000829
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 22 | 49.2 | 0.447 | 0.00000260 | 1689 |
| Missense (PolyPhen) | 12 | 20.943 | 0.57299 | 663 | ||
| Synonymous | 2.66 | 5 | 20.2 | 0.248 | 0.00000117 | 588 |
| Loss of Function | 1.35 | 2 | 5.40 | 0.371 | 2.68e-7 | 124 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. Has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. Has a preference for 5'-flap structures, and promotes symmetrical cleavage of static and migrating Holliday junctions (HJs). Resolves HJs by generating two pairs of ligatable, nicked duplex products. {ECO:0000255|HAMAP-Rule:MF_03100, ECO:0000269|PubMed:19595721, ECO:0000269|PubMed:19596235, ECO:0000269|PubMed:19596236}.;
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |