SLFN13

schlafen family member 13, the group of Schlafen family

Basic information

Region (hg38): 17:35435095-35448837

Links

ENSG00000154760 ∙ NCBI:146857 ∙ OMIM:614957 ∙ HGNC:26481 ∙ Uniprot:Q68D06 ∙ 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 SLFN13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN13 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	1	3
missense			64	9	2	75
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	11	3

Variants in SLFN13

This is a list of pathogenic ClinVar variants found in the SLFN13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35440620-T-C		not specified	Uncertain significance (Jan 23, 2023)
17-35440650-T-C		not specified	Uncertain significance (Jan 08, 2024)
17-35440659-A-T		not specified	Uncertain significance (Mar 20, 2023)
17-35440669-C-T		not specified	Uncertain significance (Apr 26, 2024)
17-35440673-T-C			Benign (May 05, 2018)
17-35440677-C-G		not specified	Uncertain significance (May 20, 2024)
17-35440722-C-A		not specified	Uncertain significance (Apr 26, 2024)
17-35440726-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-35440730-A-T		not specified	Uncertain significance (Nov 08, 2022)
17-35440732-T-C		not specified	Uncertain significance (Aug 22, 2023)
17-35440736-C-G		not specified	Uncertain significance (Feb 17, 2024)
17-35440758-A-G		not specified	Uncertain significance (Jan 23, 2023)
17-35440773-C-T		not specified	Uncertain significance (Nov 29, 2023)
17-35440788-A-C		not specified	Likely benign (May 30, 2024)
17-35440813-G-A		not specified	Uncertain significance (Dec 21, 2023)
17-35440839-G-A		not specified	Uncertain significance (Jul 06, 2022)
17-35440845-G-T		not specified	Uncertain significance (Sep 15, 2021)
17-35440852-C-T		not specified	Uncertain significance (Feb 27, 2023)
17-35440878-T-C		not specified	Uncertain significance (Aug 16, 2021)
17-35440898-C-G		not specified	Uncertain significance (Dec 22, 2023)
17-35440924-C-T		not specified	Uncertain significance (Nov 17, 2022)
17-35440972-C-T		not specified	Uncertain significance (Oct 27, 2022)
17-35441019-G-T		not specified	Uncertain significance (Sep 16, 2021)
17-35441086-C-T		not specified	Uncertain significance (Apr 20, 2023)
17-35441094-C-T		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN13	protein_coding	protein_coding	ENST00000285013	4	13742

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.00e-16	0.00391	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.688	500	459	1.09	0.0000235	5886
Missense in Polyphen		145	127.2	1.1399		1805
Synonymous	-1.76	199	170	1.17	0.00000886	1715
Loss of Function	-0.377	23	21.1	1.09	9.78e-7	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000643	0.000643
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000300	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endoribonuclease that cleaves tRNAs and rRNAs (PubMed:29563550). Cleaves tRNAs 11 nucleotides from the 3'- terminus at the acceptor stem (PubMed:29563550). Does not act on tRNA(Sec) (PubMed:29563550). Able to restrict HIV-1 virus replication; ability to inhibit HIV-1 replication is dependent on endoribonuclease activity (PubMed:29563550). {ECO:0000269|PubMed:29563550}.

Recessive Scores

• pRec: 0.0673

Intolerance Scores

• loftool: 0.550
• rvis_EVS: 2.76
• rvis_percentile_EVS: 99

Haploinsufficiency Scores

• pHI: 0.0598
• hipred: N
• hipred_score: 0.112
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0835

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slfn9

Gene ontology

• Biological process: rRNA catabolic process;tRNA catabolic process;defense response to virus;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: cytoplasm
• Molecular function: tRNA binding;endoribonuclease activity;ATP binding;zinc ion binding