SAMD12

sterile alpha motif domain containing 12, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 8:118189454-118622112

Links

ENSG00000177570 ∙ NCBI:401474 ∙ OMIM:618073 ∙ HGNC:31750 ∙ Uniprot:Q8N8I0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• benign adult familial myoclonic epilepsy (Supportive), mode of inheritance: AD
• epilepsy, familial adult myoclonic, 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Epilepsy, familial adult myoclonic, 1	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29939203

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD12 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)
• Epilepsy, familial adult myoclonic, 1 (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD12 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			9	1		10
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	10	1	0

Variants in SAMD12

This is a list of pathogenic ClinVar variants found in the SAMD12 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-118379421-A-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
8-118379424-T-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
8-118379658-A-G		Inborn genetic diseases	Uncertain significance (May 23, 2023)
8-118379658-A-T		See cases	Uncertain significance (Oct 14, 2021)
8-118379661-C-A		Epilepsy, familial adult myoclonic, 1	Uncertain significance (Apr 04, 2024)
8-118439834-G-A			Likely benign (Mar 01, 2023)
8-118439862-T-A		Inborn genetic diseases	Uncertain significance (Jan 10, 2022)
8-118439896-C-G			Uncertain significance (Apr 01, 2024)
8-118580743-C-T		Inborn genetic diseases	Uncertain significance (Aug 21, 2023)
8-118580762-G-T		Inborn genetic diseases	Uncertain significance (Apr 18, 2023)
8-118580801-G-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
8-118580837-T-C		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
8-118580867-C-T		Inborn genetic diseases	Uncertain significance (May 26, 2023)
8-118605260-G-T		Epilepsy, familial adult myoclonic, 1	Uncertain significance (Jun 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD12	protein_coding	protein_coding	ENST00000314727	4	432537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00117	0.854	125690	0	7	125697	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0826	109	107	1.02	0.00000548	1293
Missense in Polyphen		43	41.319	1.0407		483
Synonymous	-0.394	45	41.8	1.08	0.00000211	386
Loss of Function	1.26	6	10.4	0.579	6.94e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0731

Intolerance Scores

• loftool: 0.360
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.227
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd12