SLFNL1

schlafen like 1, the group of Schlafen family

Basic information

Region (hg38): 1:41015589-41023237

Links

ENSG00000171790 ∙ NCBI:200172 ∙ ∙ HGNC:26313 ∙ Uniprot:Q499Z3 ∙ 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 SLFNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFNL1 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			52	4		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	4	0

Variants in SLFNL1

This is a list of pathogenic ClinVar variants found in the SLFNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-41016132-C-T		not specified	Likely benign (Mar 25, 2024)
1-41016168-C-G		not specified	Uncertain significance (Aug 04, 2024)
1-41016171-T-C		not specified	Uncertain significance (Aug 04, 2024)
1-41016185-G-A		not specified	Likely benign (Aug 13, 2021)
1-41016196-C-A		not specified	Uncertain significance (Dec 07, 2024)
1-41017288-G-T		not specified	Uncertain significance (Aug 02, 2022)
1-41017290-C-T		not specified	Uncertain significance (Nov 28, 2024)
1-41017292-C-T		not specified	Uncertain significance (May 15, 2024)
1-41017295-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-41017326-A-G		not specified	Uncertain significance (Jun 07, 2023)
1-41017370-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-41017647-G-T		not specified	Uncertain significance (May 17, 2023)
1-41017691-A-G		not specified	Uncertain significance (Jul 14, 2024)
1-41017736-C-A		not specified	Uncertain significance (Apr 07, 2022)
1-41017754-G-A		not specified	Uncertain significance (Jun 30, 2023)
1-41017784-C-T		not specified	Uncertain significance (Feb 03, 2022)
1-41017802-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-41017805-C-T		not specified	Uncertain significance (Jul 09, 2024)
1-41017814-C-T		not specified	Uncertain significance (Nov 03, 2023)
1-41017829-C-T		not specified	Uncertain significance (Jan 19, 2024)
1-41017846-G-A		not specified	Uncertain significance (May 14, 2024)
1-41017853-C-T		not specified	Uncertain significance (Oct 20, 2023)
1-41017859-G-A		not specified	Uncertain significance (Oct 05, 2021)
1-41017895-C-T		not specified	Uncertain significance (Dec 14, 2023)
1-41017898-C-T		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFNL1	protein_coding	protein_coding	ENST00000359345	4	7641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000385	0.844	124213	14	1521	125748	0.00612

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.604	288	261	1.11	0.0000178	2612
Missense in Polyphen		83	82.888	1.0014		817
Synonymous	0.0899	115	116	0.989	0.00000827	837
Loss of Function	1.34	9	14.5	0.620	7.10e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00300	0.00299
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000544	0.000544
Finnish	0.0249	0.0243
European (Non-Finnish)	0.00761	0.00758
Middle Eastern	0.000544	0.000544
South Asian	0.000475	0.000457
Other	0.00886	0.00867

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.927
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.46

Haploinsufficiency Scores

• pHI: 0.0902
• hipred: N
• hipred_score: 0.146
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.387

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slfnl1

Gene ontology

• Molecular function: ATP binding