SLFN5

schlafen family member 5, the group of Schlafen family

Basic information

Region (hg38): 17:35243070-35273655

Links

ENSG00000166750 ∙ NCBI:162394 ∙ OMIM:614952 ∙ HGNC:28286 ∙ Uniprot:Q08AF3 ∙ 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 SLFN5 gene.

• Inborn genetic diseases (30 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN5 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			29	1	3	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	29	3	4

Variants in SLFN5

This is a list of pathogenic ClinVar variants found in the SLFN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35258721-T-C		not specified	Uncertain significance (Dec 28, 2022)
17-35258786-C-A		not specified	Uncertain significance (Jan 10, 2022)
17-35258791-G-A		not specified	Uncertain significance (Feb 06, 2023)
17-35258824-G-A		not specified	Likely benign (Feb 01, 2023)
17-35258827-C-T		not specified	Uncertain significance (Apr 07, 2023)
17-35258866-A-G			Benign (Apr 04, 2018)
17-35258901-C-T		not specified	Uncertain significance (Jan 20, 2023)
17-35258925-C-T		not specified	Uncertain significance (Nov 10, 2022)
17-35258997-A-T		not specified	Uncertain significance (Dec 08, 2023)
17-35259007-C-T		not specified	Uncertain significance (Sep 29, 2022)
17-35259133-A-G		not specified	Uncertain significance (May 03, 2023)
17-35259168-G-C		not specified	Uncertain significance (Jun 29, 2023)
17-35259213-T-G		not specified	Uncertain significance (Feb 06, 2024)
17-35259217-T-C		not specified	Uncertain significance (Dec 07, 2021)
17-35259270-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-35259287-G-T		not specified	Uncertain significance (Jan 03, 2024)
17-35259366-T-C		not specified	Uncertain significance (Dec 15, 2023)
17-35259394-C-T		not specified	Uncertain significance (Aug 04, 2021)
17-35259420-G-C		not specified	Uncertain significance (Oct 05, 2023)
17-35259436-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-35259437-G-A			Likely benign (Sep 01, 2022)
17-35259519-G-A			Benign (Apr 04, 2018)
17-35259526-A-G		not specified	Uncertain significance (Dec 19, 2023)
17-35259667-G-A		not specified	Likely benign (Nov 15, 2021)
17-35259709-G-A			Benign (Feb 25, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN5	protein_coding	protein_coding	ENST00000299977	4	30620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-12	0.0576	125686	0	59	125745	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.345	456	477	0.956	0.0000254	5855
Missense in Polyphen		90	111.95	0.8039		1485
Synonymous	0.310	178	183	0.971	0.00000977	1730
Loss of Function	0.308	19	20.5	0.927	9.60e-7	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000520	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.000111	0.0000924
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.0000548	0.0000544
South Asian	0.000691	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role in hematopoietic cell differentiation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.479
• rvis_EVS: 0.63
• rvis_percentile_EVS: 83.57

Haploinsufficiency Scores

• pHI: 0.0637
• hipred: N
• hipred_score: 0.112
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.170

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slfn5

Gene ontology

• Biological process: cell differentiation
• Cellular component: nucleus
• Molecular function: ATP binding