SAMD3

sterile alpha motif domain containing 3, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 6:130144314-130365425

Links

ENSG00000164483 ∙ NCBI:154075 ∙ ∙ HGNC:21574 ∙ Uniprot:Q8N6K7 ∙ 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 SAMD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD3 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	4		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	4	0

Variants in SAMD3

This is a list of pathogenic ClinVar variants found in the SAMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-130144542-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-130144546-C-T		not specified	Uncertain significance (Mar 11, 2024)
6-130144666-A-G		not specified	Uncertain significance (Mar 20, 2023)
6-130144677-A-G		not specified	Uncertain significance (Mar 11, 2024)
6-130144702-C-T		not specified	Likely benign (Mar 24, 2023)
6-130144705-C-T		not specified	Uncertain significance (Jul 26, 2022)
6-130144771-T-G		not specified	Uncertain significance (Aug 09, 2021)
6-130145380-A-G		not specified	Uncertain significance (Feb 06, 2023)
6-130146035-A-T		not specified	Likely benign (Aug 13, 2021)
6-130146036-T-A		not specified	Uncertain significance (Jul 27, 2021)
6-130146105-T-C		not specified	Uncertain significance (Jan 16, 2024)
6-130146115-A-G		not specified	Uncertain significance (Oct 13, 2023)
6-130146133-T-G		not specified	Uncertain significance (Feb 16, 2023)
6-130146180-A-G		not specified	Uncertain significance (May 14, 2024)
6-130154844-A-G		not specified	Uncertain significance (Jun 30, 2023)
6-130154994-T-A		not specified	Uncertain significance (Jun 10, 2024)
6-130175851-A-C		not specified	Uncertain significance (Jun 07, 2024)
6-130175902-C-T		not specified	Uncertain significance (Apr 25, 2022)
6-130184126-G-C		not specified	Uncertain significance (Mar 29, 2023)
6-130184159-C-T		not specified	Uncertain significance (Oct 13, 2023)
6-130184465-T-C		not specified	Uncertain significance (Nov 21, 2022)
6-130184534-C-G		not specified	Uncertain significance (Oct 10, 2023)
6-130184615-A-G		not specified	Uncertain significance (Jan 16, 2024)
6-130209508-C-A		not specified	Uncertain significance (Sep 22, 2022)
6-130209568-C-T		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD3	protein_coding	protein_coding	ENST00000368134	10	221111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-15	0.0474	125463	0	283	125746	0.00113

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.113	261	266	0.981	0.0000128	3466
Missense in Polyphen		72	78.949	0.91198		1031
Synonymous	-0.712	106	97.1	1.09	0.00000517	916
Loss of Function	0.645	25	28.7	0.870	0.00000171	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00549	0.00545
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00215	0.00212
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000909	0.000906
Middle Eastern	0.00215	0.00212
South Asian	0.000587	0.000555
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Pathway: TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.943
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.263
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.721

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd3

Gene ontology

• Molecular function: protein binding