SLFN12L

schlafen family member 12 like, the group of Schlafen family

Basic information

Region (hg38): 17:35464249-35537683

Links

ENSG00000205045 ∙ NCBI:100506736 ∙ OMIM:614956 ∙ HGNC:33920 ∙ Uniprot:Q6IEE8 ∙ 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 SLFN12L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN12L 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			24	2	2	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	2

Variants in SLFN12L

This is a list of pathogenic ClinVar variants found in the SLFN12L region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35474969-C-T		not specified	Uncertain significance (Feb 21, 2024)
17-35474970-G-A		not specified	Likely benign (Apr 09, 2024)
17-35475024-G-A		not specified	Uncertain significance (Apr 22, 2022)
17-35475044-A-G		not specified	Uncertain significance (May 16, 2022)
17-35475075-C-G		not specified	Uncertain significance (Feb 05, 2024)
17-35475183-T-G		not specified	Uncertain significance (Jun 11, 2021)
17-35475209-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-35475253-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-35475254-A-C		not specified	Likely benign (Sep 01, 2021)
17-35475257-T-C		not specified	Uncertain significance (Jun 07, 2024)
17-35475278-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-35475279-G-C		not specified	Uncertain significance (Mar 29, 2022)
17-35475302-G-T		not specified	Uncertain significance (Nov 08, 2022)
17-35475320-T-C		not specified	Uncertain significance (Jun 28, 2022)
17-35475352-G-T		not specified	Uncertain significance (Feb 12, 2024)
17-35478092-A-T		not specified	Likely benign (Jul 12, 2023)
17-35478122-C-T		not specified	Uncertain significance (Dec 21, 2022)
17-35478170-G-A		not specified	Uncertain significance (May 27, 2022)
17-35478183-A-G		not specified	Uncertain significance (Mar 15, 2024)
17-35479245-G-A		not specified	Uncertain significance (Jul 19, 2023)
17-35479281-A-T		not specified	Uncertain significance (Nov 19, 2022)
17-35479459-C-A		not specified	Uncertain significance (Dec 17, 2023)
17-35479525-T-A			Benign (Aug 15, 2017)
17-35479590-T-A		not specified	Uncertain significance (Jan 03, 2024)
17-35479591-C-T		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN12L	protein_coding	protein_coding	ENST00000260908	4	73613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.66e-11	0.0397	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0225	286	287	0.996	0.0000135	3862
Missense in Polyphen		78	85.64	0.91079		1168
Synonymous	-0.297	110	106	1.04	0.00000522	1077
Loss of Function	-0.237	15	14.0	1.07	7.55e-7	211

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

Intolerance Scores

• rvis_EVS: 2.77
• rvis_percentile_EVS: 99.01

Haploinsufficiency Scores

• pHI: 0.0817
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.156

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slfn4
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: ATP binding