SLFN14

schlafen family member 14, the group of Schlafen family

Basic information

Region (hg38): 17:35543984-35560819

Links

ENSG00000236320 ∙ NCBI:342618 ∙ OMIM:614958 ∙ HGNC:32689 ∙ Uniprot:P0C7P3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• platelet-type bleeding disorder 20 (Strong), mode of inheritance: AD
• platelet-type bleeding disorder 20 (Supportive), mode of inheritance: AD
• platelet-type bleeding disorder 20 (Moderate), mode of inheritance: AD
• platelet-type bleeding disorder 20 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bleeding disorder, platelet-type, 20	AR	Hematologic	Individuals have increased bleeding tendency, and awareness may allow preventive measures and early management of bleeding complications	Hematologic	26280575; 26769223

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLFN14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN14 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				6	5	11
missense		1	55	6	8	70
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					8	8
Total	0	1	60	12	21

Variants in SLFN14

This is a list of pathogenic ClinVar variants found in the SLFN14 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35548243-T-A		Platelet-type bleeding disorder 20	Benign (Jul 15, 2021)
17-35548254-C-T		SLFN14-related disorder	Benign/Likely benign (May 24, 2019)
17-35548265-G-A		Platelet-type bleeding disorder 20	Benign (Jul 15, 2021)
17-35548286-C-G			Uncertain significance (Nov 06, 2017)
17-35548292-A-G		Abnormal bleeding;Thrombocytopenia	Uncertain significance (May 01, 2020)
17-35548340-TA-T		Platelet-type bleeding disorder 20	Uncertain significance (Sep 03, 2021)
17-35548353-G-A		Inborn genetic diseases	Likely benign (Feb 06, 2024)
17-35548402-T-C		Inborn genetic diseases	Uncertain significance (May 21, 2024)
17-35548418-C-T		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
17-35548426-G-A			Uncertain significance (Nov 12, 2019)
17-35548435-A-C		Inborn genetic diseases	Uncertain significance (Jun 10, 2024)
17-35548506-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Dec 01, 2022)
17-35548523-A-G		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
17-35548559-G-T		not specified • Inborn genetic diseases	Uncertain significance (Jul 05, 2022)
17-35548669-T-A		SLFN14-related disorder	Likely benign (Dec 11, 2023)
17-35548687-A-G		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
17-35548717-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
17-35548762-G-A		Inborn genetic diseases	Uncertain significance (Nov 23, 2021)
17-35548771-A-G		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
17-35548778-A-C		Inborn genetic diseases	Uncertain significance (Apr 20, 2024)
17-35548791-G-C		SLFN14-related disorder	Benign/Likely benign (Jan 24, 2020)
17-35548804-C-T		Inborn genetic diseases	Uncertain significance (Jul 12, 2022)
17-35548824-AG-A		Platelet-type bleeding disorder 20	Uncertain significance (Aug 10, 2018)
17-35548832-G-A		Platelet-type bleeding disorder 20	Uncertain significance (Aug 10, 2018)
17-35548847-C-A		Inborn genetic diseases	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN14	protein_coding	protein_coding	ENST00000415846	4	9974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.51e-9	0.929	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	318	465	0.684	0.0000225	6013
Missense in Polyphen		89	137.81	0.64581		1859
Synonymous	2.20	134	170	0.786	0.00000838	1732
Loss of Function	1.90	18	29.1	0.619	0.00000152	403

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: Protein SLFN14: Shows no ribosome-associated and endoribonuclease activities. {ECO:0000269|PubMed:25996083}.

Intolerance Scores

• rvis_EVS: 2.71
• rvis_percentile_EVS: 98.93

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.310

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slfn14

Gene ontology

• Biological process: mRNA catabolic process;rRNA catabolic process;platelet maturation;cellular response to magnesium ion;cellular response to manganese ion;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: nucleus;cytoplasm
• Molecular function: endoribonuclease activity;ATP binding;ribosome binding