SLFN12

protein-coding

schlafen family member 12, the group of Schlafen family

Gene summary

Enables RNA nuclease activity and ribosome binding activity. Involved in apoptotic signaling pathway and rRNA catabolic process. Part of cytosol and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018042.5

Inheritance

—

ClinVar variants

U:76B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.81

Max pathogenic AF

—

Genomic locus

chr17:35,409,465-35,433,475

External References & Databases

Ensembl (ENSG00000172123)

Transcript & Mutation Effects

hg38 • Region Span ~24.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLFN12 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 86

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018042.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			76 clinvar	10 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	76	10	0	86

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018042.5	RefSeq	NP_060512.3	3	MANE Select
ENST00000304905.10	Ensembl	ENSP00000302077.5	3	MANE Select
NM_001289009.2	RefSeq	NP_001275938.1	3	Standard
ENST00000394562.5	Ensembl	ENSP00000378063.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

ATP binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394562
Coding exons: 3
Length: 22224
Individuals with no LoFs: 125202
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125204
p: 0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0961	293	298	0.984	0.0000144	3827
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000062	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0696

Intolerance Scores

LoFtool: 0.950
RVIS EVS: 1.33
RVIS percentile EVS: 94.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0508

Gene Damage Prediction

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