SLX1B

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

Basic information

Region (hg38): 16:29454533-29458219

Previous symbols: [ "GIYD2" ]

Links

ENSG00000181625 ∙ NCBI:79008 ∙ OMIM:615823 ∙ HGNC:28748 ∙ 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 SLX1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLX1B 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SLX1B

This is a list of pathogenic ClinVar variants found in the SLX1B region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29457641-G-A		not specified	Uncertain significance (Mar 10, 2025)
16-29457656-C-T		not specified	Uncertain significance (Nov 12, 2024)
16-29457930-G-T		not specified	Uncertain significance (Jun 16, 2023)
16-29457960-T-A		not specified	Uncertain significance (Dec 12, 2023)
16-29457979-C-G		not specified	Uncertain significance (May 23, 2024)
16-29458107-G-A		not specified	Uncertain significance (Aug 11, 2024)
16-29458117-A-G		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLX1B	protein_coding	protein_coding	ENST00000330181	6	3719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0442	0.684	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	6	23.2	0.259	9.87e-7	1739
Missense in Polyphen		4	6.5195	0.61354		681
Synonymous	1.90	2	9.44	0.212	4.11e-7	606
Loss of Function	0.556	2	3.05	0.656	1.30e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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;Phase II - Conjugation of compounds;Homology Directed Repair;dopamine degradation;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules;serotonin degradation;superpathway of tryptophan utilization;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: 0.258
• ghis: 0.468

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	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

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