SLFN12

schlafen family member 12, the group of Schlafen family

Basic information

Region (hg38): 17:35409465-35433475

Links

ENSG00000172123 ∙ NCBI:55106 ∙ OMIM:614955 ∙ HGNC:25500 ∙ Uniprot:Q8IYM2 ∙ 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 SLFN12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLFN12 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			29	6		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	6	0

Variants in SLFN12

This is a list of pathogenic ClinVar variants found in the SLFN12 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-35411351-C-G		not specified	Uncertain significance (Oct 13, 2023)
17-35411465-G-A		not specified	Likely benign (May 09, 2023)
17-35411519-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-35411561-A-T		not specified	Likely benign (Jul 14, 2023)
17-35411724-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-35411797-C-G		not specified	Uncertain significance (May 01, 2024)
17-35411909-G-A		not specified	Uncertain significance (May 30, 2023)
17-35420276-G-A		not specified	Uncertain significance (Sep 25, 2023)
17-35420339-G-A		not specified	Likely benign (Jun 21, 2022)
17-35420343-T-G		not specified	Uncertain significance (Jan 23, 2023)
17-35422024-C-G		not specified	Uncertain significance (Mar 25, 2024)
17-35422107-C-G		not specified	Uncertain significance (Apr 09, 2024)
17-35422118-G-T		not specified	Uncertain significance (Aug 01, 2022)
17-35422134-A-C		not specified	Uncertain significance (Feb 06, 2023)
17-35422197-T-C		not specified	Uncertain significance (May 18, 2023)
17-35422199-C-A		not specified	Uncertain significance (Feb 06, 2023)
17-35422223-C-T		not specified	Likely benign (Jan 23, 2023)
17-35422238-A-G		not specified	Uncertain significance (May 04, 2023)
17-35422266-T-G		not specified	Uncertain significance (Jan 09, 2024)
17-35422268-A-T		not specified	Likely benign (Nov 17, 2022)
17-35422325-C-T		not specified	Uncertain significance (Sep 22, 2022)
17-35422356-A-G		not specified	Uncertain significance (Aug 28, 2021)
17-35422371-C-G		not specified	Uncertain significance (Feb 06, 2023)
17-35422400-G-A		not specified	Uncertain significance (Jul 14, 2022)
17-35422457-T-C		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLFN12	protein_coding	protein_coding	ENST00000394562	3	22224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.69e-7	0.404	125202	0	2	125204	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0961	293	298	0.984	0.0000144	3827
Missense in Polyphen		70	78.1	0.89629		1054
Synonymous	-0.0556	112	111	1.01	0.00000560	1054
Loss of Function	0.634	11	13.5	0.814	7.57e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000622	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000622	0.0000544
South Asian	0.0000328	0.0000328
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0696

Intolerance Scores

• loftool: 0.950
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.21

Haploinsufficiency Scores

• pHI: 0.0418
• hipred: N
• hipred_score: 0.148
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0508

Gene Damage Prediction

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

Gene ontology

• Molecular function: ATP binding