SAMSN1

SAM domain, SH3 domain and nuclear localization signals 1, the group of SAM and SH3 domain containing|Sterile alpha motif domain containing

Basic information

Region (hg38): 21:14485228-14658821

Links

ENSG00000155307 ∙ NCBI:64092 ∙ OMIM:607978 ∙ HGNC:10528 ∙ Uniprot:Q9NSI8 ∙ 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 SAMSN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMSN1 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	0	0	17	1	1

Variants in SAMSN1

This is a list of pathogenic ClinVar variants found in the SAMSN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-14485916-T-A		not specified	Uncertain significance (Apr 25, 2023)
21-14485962-T-C		not specified	Uncertain significance (Jan 06, 2023)
21-14485986-C-T		not specified	Uncertain significance (Apr 26, 2024)
21-14498527-C-A		not specified	Uncertain significance (Dec 03, 2021)
21-14500587-C-A		not specified	Uncertain significance (May 15, 2024)
21-14500608-T-C		not specified	Uncertain significance (Jul 09, 2021)
21-14500614-G-A		not specified	Uncertain significance (Feb 06, 2024)
21-14500647-A-G		not specified	Uncertain significance (May 02, 2023)
21-14500686-G-A		not specified	Uncertain significance (Jun 30, 2023)
21-14500687-T-A		not specified	Uncertain significance (Jun 30, 2023)
21-14510301-T-C			Benign (Jun 23, 2018)
21-14510372-G-A		not specified	Uncertain significance (Jan 18, 2022)
21-14510387-C-T		not specified	Uncertain significance (Jul 09, 2021)
21-14512495-G-T		not specified	Uncertain significance (May 24, 2023)
21-14512509-G-C		not specified	Uncertain significance (May 28, 2024)
21-14512521-A-G		not specified	Uncertain significance (Jan 30, 2024)
21-14516908-G-T		not specified	Uncertain significance (Dec 20, 2021)
21-14516936-T-C		not specified	Uncertain significance (Jul 13, 2022)
21-14521185-T-G		not specified	Uncertain significance (Apr 22, 2022)
21-14521187-C-T		not specified	Uncertain significance (Dec 08, 2021)
21-14521188-G-A		not specified	Uncertain significance (May 24, 2023)
21-14582274-C-A			Likely benign (Aug 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMSN1	protein_coding	protein_coding	ENST00000285670	8	98175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-11	0.205	124832	0	28	124860	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.304	216	229	0.943	0.0000113	2923
Missense in Polyphen		87	91.837	0.94733		1183
Synonymous	-0.625	87	79.9	1.09	0.00000386	783
Loss of Function	0.746	18	21.8	0.827	0.00000111	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000122
Ashkenazi Jewish	0.000199	0.000199
East Asian	0.0000564	0.0000556
Finnish	0.0000929	0.0000928
European (Non-Finnish)	0.000160	0.000159
Middle Eastern	0.0000564	0.0000556
South Asian	0.0000667	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of B-cell activation. Down-regulates cell proliferation (in vitro). Promotes RAC1-dependent membrane ruffle formation and reorganization of the actin cytoskeleton. Regulates cell spreading and cell polarization. Stimulates HDAC1 activity. Regulates LYN activity by modulating its tyrosine phosphorylation (By similarity). {ECO:0000250, ECO:0000269|PubMed:15381729}.
• Pathway: Integrated Lung Cancer Pathway;TYROBP Causal Network (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.566
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.289
• ghis: 0.448

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.432

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samsn1
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of adaptive immune response;negative regulation of peptidyl-tyrosine phosphorylation;negative regulation of B cell activation
• Cellular component: ruffle;nucleus;cytosol;plasma membrane
• Molecular function: phosphotyrosine residue binding;RNA binding