SAMD9L
Basic information
Region (hg38): 7:93130056-93148385
Previous symbols: [ "C7orf6" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Ataxia-pancytopenia syndrome; Monosomy 7 myelodysplasia and leukemia syndrome 1 | AD | Allergy/Immunology/Infectious; Hematologic; Oncologic | Ataxia-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 disease | Allergy/Immunology/Infectious; Hematologic; Neurologic; Oncologic | 283689; 27259050; 30046003; 30322869; 35310830 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 511 | 519 | ||||
missense | 16 | 1291 | 98 | 1416 | ||
nonsense | 47 | 50 | ||||
start loss | 2 | 2 | ||||
frameshift | 51 | 57 | ||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 4 | 23 | 1400 | 611 | 7 |
Highest pathogenic variant AF is 0.00000929842
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SAMD9L | protein_coding | protein_coding | ENST00000318238 | 1 | 18315 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.57e-15 | 0.997 | 124982 | 1 | 755 | 125738 | 0.00301 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.63 | 661 | 790 | 0.836 | 0.0000385 | 10531 |
Missense in Polyphen | 159 | 196.97 | 0.80725 | 2746 | ||
Synonymous | -0.511 | 294 | 283 | 1.04 | 0.0000135 | 2889 |
Loss of Function | 2.86 | 32 | 54.9 | 0.583 | 0.00000297 | 761 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00325 | 0.00324 |
Ashkenazi Jewish | 0.00459 | 0.00457 |
East Asian | 0.000654 | 0.000653 |
Finnish | 0.00569 | 0.00556 |
European (Non-Finnish) | 0.00397 | 0.00388 |
Middle Eastern | 0.000654 | 0.000653 |
South Asian | 0.000915 | 0.000915 |
Other | 0.00247 | 0.00245 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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