SAMD9L

sterile alpha motif domain containing 9 like, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 7:93130056-93148385

Previous symbols: [ "C7orf6" ]

Links

ENSG00000177409NCBI:219285OMIM:611170HGNC:1349Uniprot:Q8IVG5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • ataxia-pancytopenia syndrome (Strong), mode of inheritance: AD
  • ataxia-pancytopenia syndrome (Limited), mode of inheritance: AD
  • ataxia-pancytopenia syndrome (Supportive), mode of inheritance: AD
  • ataxia-pancytopenia syndrome (Definitive), mode of inheritance: AD
  • spinocerebellar ataxia 49 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ataxia-pancytopenia syndrome; Monosomy 7 myelodysplasia and leukemia syndrome 1ADAllergy/Immunology/Infectious; Hematologic; OncologicAtaxia-pancytopenia syndrome can include pancytopenia and related infectious risks, and awareness may allow prophylactic measures and early and aggressive treatment of infections and hematologic issues; Individuals have been descriebd with hematologic malignancies, and awareness may allow surveillance and prompt detection and management; Monosomy 7 myelodysplasia and leukemia syndrome 1 involves germline genetic anomaly as well as associated somatic loss of chromosome 7, and results in increased risk of hematologic malignancy such that awareness may allow early diagnosis and management of diseaseAllergy/Immunology/Infectious; Hematologic; Neurologic; Oncologic283689; 27259050; 30046003; 30322869; 35310830

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD9L gene.

  • Inborn_genetic_diseases (1432 variants)
  • not_provided (1113 variants)
  • Ataxia-pancytopenia_syndrome (90 variants)
  • SAMD9L-related_disorder (89 variants)
  • not_specified (84 variants)
  • Monosomy_7_myelodysplasia_and_leukemia_syndrome_1 (42 variants)
  • Spinocerebellar_ataxia_49 (39 variants)
  • Microcephaly (3 variants)
  • Hereditary_cancer-predisposing_syndrome (1 variants)
  • interferonopathy (1 variants)
  • Intellectual_disability (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 SAMD9L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152703.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
511
clinvar
519
missense
4
clinvar
16
clinvar
1291
clinvar
98
clinvar
7
clinvar
1416
nonsense
2
clinvar
47
clinvar
1
clinvar
50
start loss
2
2
frameshift
5
clinvar
51
clinvar
1
clinvar
57
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 4 23 1400 611 7

Highest pathogenic variant AF is 0.00000929842

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAMD9Lprotein_codingprotein_codingENST00000318238 118315
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
5.57e-150.99712498217551257380.00301
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.636617900.8360.000038510531
Missense in Polyphen159196.970.807252746
Synonymous-0.5112942831.040.00001352889
Loss of Function2.863254.90.5830.00000297761

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003250.00324
Ashkenazi Jewish0.004590.00457
East Asian0.0006540.000653
Finnish0.005690.00556
European (Non-Finnish)0.003970.00388
Middle Eastern0.0006540.000653
South Asian0.0009150.000915
Other0.002470.00245

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in endosome fusion. Mediates down- regulation of growth factor signaling via internalization of growth factor receptors. {ECO:0000250|UniProtKB:Q69Z37}.;

Recessive Scores

pRec
0.0905

Intolerance Scores

loftool
rvis_EVS
-0.03
rvis_percentile_EVS
50.56

Haploinsufficiency Scores

pHI
0.122
hipred
N
hipred_score
0.132
ghis
0.514

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.252

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Samd9l
Phenotype
immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process
endosomal vesicle fusion
Cellular component
cytoplasm;early endosome
Molecular function
protein binding