SLFN11

schlafen family member 11, the group of Schlafen family

Basic information

Region (hg38): 17:35350305-35373701

Links

ENSG00000172716 ∙ NCBI:91607 ∙ OMIM:614953 ∙ HGNC:26633 ∙ Uniprot:Q7Z7L1 ∙ 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 SLFN11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN11 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				1	1	2
missense			55	11	2	68
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	12	3

Variants in SLFN11

This is a list of pathogenic ClinVar variants found in the SLFN11 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35352361-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-35352369-C-G		not specified	Uncertain significance (Mar 20, 2023)
17-35352372-G-A		not specified	Likely benign (Nov 13, 2024)
17-35352389-T-G		not specified	Uncertain significance (Aug 12, 2021)
17-35352459-A-G		Moyamoya angiopathy	Likely pathogenic (-)
17-35352498-C-T		not specified	Uncertain significance (Apr 13, 2022)
17-35352499-G-A		not specified	Uncertain significance (May 20, 2024)
17-35352540-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-35352612-T-G		not specified	Uncertain significance (Nov 13, 2024)
17-35352615-G-A		not specified	Uncertain significance (Nov 13, 2024)
17-35352616-C-T			Benign (Aug 08, 2018)
17-35352669-C-T		not specified	Uncertain significance (Aug 08, 2023)
17-35352670-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-35352695-C-T		not specified	Uncertain significance (Oct 22, 2024)
17-35352697-T-C		not specified	Likely benign (Dec 08, 2023)
17-35352709-C-A		not specified	Likely benign (Jun 11, 2021)
17-35352729-C-T		not specified	Likely benign (Aug 13, 2021)
17-35352730-G-C		not specified	Uncertain significance (Mar 29, 2022)
17-35352844-A-T		not specified	Uncertain significance (Dec 21, 2022)
17-35352894-G-A		not specified	Uncertain significance (May 07, 2024)
17-35352913-G-T		not specified	Uncertain significance (Oct 29, 2024)
17-35352982-C-A		not specified	Likely benign (Aug 02, 2021)
17-35352984-C-T		not specified	Likely benign (Aug 02, 2021)
17-35352996-C-G		not specified	Uncertain significance (Sep 29, 2022)
17-35353005-C-G		not specified	Likely benign (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN11	protein_coding	protein_coding	ENST00000394566	4	23397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.22e-19	0.00110	125713	0	32	125745	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.327	480	460	1.04	0.0000244	5894
Missense in Polyphen		122	124.06	0.98336		1781
Synonymous	-1.63	199	172	1.16	0.00000924	1744
Loss of Function	-0.566	26	23.1	1.13	0.00000112	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000285	0.000278
Ashkenazi Jewish	0.000108	0.0000992
East Asian	0.000290	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000290	0.000272
South Asian	0.0000693	0.0000653
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of DNA replication that promotes cell death in response to DNA damage (PubMed:22927417, PubMed:26658330, PubMed:29395061). Acts as a guardian of the genome by killing cells with defective replication (PubMed:29395061). Persistently blocks stressed replication forks by opening chromatin across replication initiation sites at stressed replication forks, possibly leading to unwind DNA ahead of the MCM helicase and block fork progression, ultimately leading to cell death (PubMed:29395061). Acts independently of ATR (PubMed:29395061). Also acts as an interferon (IFN)-induced antiviral protein which acts as an inhibitor of retrovirus protein synthesis (PubMed:23000900). Specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1) by acting as a specific inhibitor of the synthesis of retroviruses encoded proteins in a codon-usage-dependent manner (PubMed:23000900). Binds to tRNAs and exploits the unique viral codon bias towards A/T nucleotides (PubMed:23000900). The exact inhibition mechanism is unclear: may either sequester tRNAs, prevent their maturation via post-transcriptional processing or may accelerate their deacylation (PubMed:23000900). Does not inhibit reverse transcription, integration or production and nuclear export of viral RNA (PubMed:23000900). {ECO:0000269|PubMed:22927417, ECO:0000269|PubMed:23000900, ECO:0000269|PubMed:26658330, ECO:0000269|PubMed:29395061}.

Intolerance Scores

• loftool: 0.316
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.71

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.148
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Gene ontology

• Biological process: cellular response to DNA damage stimulus;negative regulation of DNA replication;positive regulation of cell death;replication fork arrest;defense response to virus;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nucleoplasm;cytosol;aggresome;site of DNA damage
• Molecular function: tRNA binding;helicase activity;protein binding;ATP binding;ATPase activity