SLX1A

SLX1 homolog A, structure-specific endonuclease subunit, the group of GIY-YIG endonuclease domain containing

Basic information

Region (hg38): 16:30193875-30197566

Previous symbols: [ "GIYD1" ]

Links

ENSG00000132207 ∙ NCBI:548593 ∙ OMIM:615822 ∙ HGNC:20922 ∙ Uniprot:Q9BQ83 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLX1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLX1A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in SLX1A

This is a list of pathogenic ClinVar variants found in the SLX1A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-30194750-C-G		not specified	Uncertain significance (Sep 07, 2022)
16-30194783-G-A		not specified	Uncertain significance (Apr 20, 2024)
16-30194789-C-G		not specified	Uncertain significance (Feb 27, 2024)
16-30194907-C-A		not specified	Uncertain significance (Apr 20, 2024)
16-30194914-C-A		not specified	Uncertain significance (Oct 10, 2023)
16-30194923-G-T		not specified	Uncertain significance (Jun 05, 2024)
16-30194950-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-30194962-C-G		not specified	Uncertain significance (Apr 12, 2024)
16-30194996-G-A		not specified	Uncertain significance (Oct 13, 2023)
16-30195003-G-A		not specified	Uncertain significance (Mar 15, 2024)
16-30195058-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-30197061-G-A		not specified	Uncertain significance (Nov 09, 2021)
16-30197073-C-T		not specified	Uncertain significance (May 30, 2024)
16-30197272-G-C		not specified	Uncertain significance (Jun 13, 2024)
16-30197297-C-T			Likely benign (Mar 01, 2023)
16-30197315-G-A			Likely benign (Jul 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLX1A	protein_coding	protein_coding	ENST00000251303	6	3675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.123	0.788	120672	0	2	120674	0.00000829

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	22	49.2	0.447	0.00000260	1689
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000134	0.000134
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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;Homology Directed Repair;Resolution of D-loop Structures through Holliday Junction Intermediates;Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR) (Consensus)

Haploinsufficiency Scores

• pHI: 0.999
• hipred: N
• hipred_score: 0.318
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slx1b
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• 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;telomeric D-loop disassembly;nucleic acid phosphodiester bond hydrolysis;t-circle formation;negative regulation of telomere maintenance via telomere lengthening;positive regulation of t-circle formation
• Cellular component: nucleoplasm;Slx1-Slx4 complex
• Molecular function: endodeoxyribonuclease activity;protein binding;crossover junction endodeoxyribonuclease activity;5'-flap endonuclease activity;metal ion binding