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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): 21:14485227-14658821

Links

ENSG00000155307NCBI:64092OMIM:607978HGNC:10528Uniprot:Q9NSI8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMSN1 gene.

  • Inborn genetic diseases (15 variants)
  • not provided (2 variants)

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
14
clinvar
1
clinvar
15
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
2
Total 0 0 15 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 Inborn genetic diseases Uncertain significance (Apr 25, 2023)2540181
21-14485962-T-C Inborn genetic diseases Uncertain significance (Jan 06, 2023)2474126
21-14498527-C-A Inborn genetic diseases Uncertain significance (Dec 03, 2021)2263336
21-14500608-T-C Inborn genetic diseases Uncertain significance (Jul 09, 2021)2235948
21-14500647-A-G Inborn genetic diseases Uncertain significance (May 02, 2023)2568032
21-14500686-G-A Inborn genetic diseases Uncertain significance (Jun 30, 2023)2605148
21-14500687-T-A Inborn genetic diseases Uncertain significance (Jun 30, 2023)2605147
21-14510301-T-C Benign (Jun 23, 2018)731855
21-14510372-G-A Inborn genetic diseases Uncertain significance (Jan 18, 2022)2381084
21-14510387-C-T Inborn genetic diseases Uncertain significance (Jul 09, 2021)2361829
21-14512495-G-T Inborn genetic diseases Uncertain significance (May 24, 2023)2551703
21-14516908-G-T Inborn genetic diseases Uncertain significance (Dec 20, 2021)2384047
21-14516936-T-C Inborn genetic diseases Uncertain significance (Jul 13, 2022)2301586
21-14521185-T-G Inborn genetic diseases Uncertain significance (Apr 22, 2022)2400557
21-14521187-C-T Inborn genetic diseases Uncertain significance (Dec 08, 2021)2398150
21-14521188-G-A Inborn genetic diseases Uncertain significance (May 24, 2023)2551704
21-14582274-C-A Likely benign (Aug 28, 2018)718365

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAMSN1protein_codingprotein_codingENST00000285670 898175
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.04e-110.2051248320281248600.000112
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3042162290.9430.00001132923
Missense in Polyphen8791.8370.947331183
Synonymous-0.6258779.91.090.00000386783
Loss of Function0.7461821.80.8270.00000111290

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000122
Ashkenazi Jewish0.0001990.000199
East Asian0.00005640.0000556
Finnish0.00009290.0000928
European (Non-Finnish)0.0001600.000159
Middle Eastern0.00005640.0000556
South Asian0.00006670.0000654
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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