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SAMD9

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

Basic information

Region (hg38): 7:93099513-93118023

Previous symbols: [ "C7orf5" ]

Links

ENSG00000205413 ∙ NCBI:54809 ∙ OMIM:610456 ∙ HGNC:1348 ∙ Uniprot:Q5K651 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 5.

Transcript IDProtein IDCoding exonsMANE SelectMANE Plus Clinical
NM_017654.4NP_060124.21yes-
ENST00000379958.3ENSP00000369292.21yes-
NM_001193307.2NP_001180236.11--
ENST00000446617.1ENSP00000414529.11--

Phenotypes

GenCC

Source: genCC

  • MIRAGE syndrome (Definitive), mode of inheritance: AD
  • normophosphatemic familial tumoral calcinosis (Moderate), mode of inheritance: AR
  • monosomy 7 myelodysplasia and leukemia syndrome 2 (Limited), mode of inheritance: AD
  • normophosphatemic familial tumoral calcinosis (Limited), mode of inheritance: AR
  • SAMD9-related spectrum and myeloid neoplasm risk (Definitive), mode of inheritance: AD
  • MIRAGE syndrome (Moderate), mode of inheritance: AD
  • normophosphatemic familial tumoral calcinosis (Moderate), mode of inheritance: AR
  • monosomy 7 myelodysplasia and leukemia syndrome 2 (Limited), mode of inheritance: Unknown
  • MIRAGE syndrome (Strong), mode of inheritance: AD
  • normophosphatemic familial tumoral calcinosis (Strong), mode of inheritance: AR
  • normophosphatemic familial tumoral calcinosis (Supportive), mode of inheritance: AR
  • MIRAGE syndrome (Supportive), mode of inheritance: AD
  • MIRAGE syndrome (Strong), mode of inheritance: AD
  • monosomy 7 myelodysplasia and leukemia syndrome 2 (Strong), mode of inheritance: AD
  • normophosphatemic familial tumoral calcinosis (Moderate), mode of inheritance: AR
  • MIRAGE syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Mirage syndrome; Monosomy 7 myelodysplasia and leukemia syndrome 2; Tumoral calcinosis, normophosphatemic, familialAD/ARAllergy/Immunology/Infectious; Endocrine; Hematologic; Musculoskeletal; OncologicMirage syndrome can include anemia and thrombocytopenia requiring transfusions; Individuals can have severe and recurrent infections, and awareness may allow preventive measures and early and aggressive treatment of infections; Individuals may have salt-wasting adrenal hypoplasia, and awareness may allow prompt recognition and treatment to manage electrolyte and endocrine sequelae; For individuals with Tumoral calcinosis, surveillance/early treatment of tumoral calcinosis may reduce morbidity; Monosomy 7 myelodysplasia and leukemia syndrome 2 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; Dental; Dermatologic; Endocrine; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic3366131; 15133511; 16960814; 18094730; 27182967; 28487541; 30046003; 30322869
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ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD9 gene.

  • Inborn_genetic_diseases (1852 variants)
  • not_provided (1383 variants)
  • not_specified (139 variants)
  • SAMD9-related_disorder (109 variants)
  • MIRAGE_syndrome (73 variants)
  • Monosomy_7_myelodysplasia_and_leukemia_syndrome_2 (59 variants)
  • Normophosphatemic_familial_tumoral_calcinosis (43 variants)
  • Hereditary_cancer-predisposing_syndrome (3 variants)
  • See_cases (3 variants)
  • Intellectual_disability (2 variants)
  • Familial_thoracic_aortic_aneurysm_and_aortic_dissection (1 variants)
  • Myelodysplastic_syndrome (1 variants)
  • Hereditary_cancer (1 variants)
  • Diffuse_midline_glioma,_H3_K27-altered (1 variants)
  • Ataxia-pancytopenia_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_017654.4. 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
3
clinvar
724
clinvar
1
clinvar
 728
missense
8
clinvar
28
clinvar
1556
clinvar
96
clinvar
7
clinvar
 1695
nonsense
5
clinvar
63
clinvar
1
clinvar
 69
start loss
2
2
frameshift
1
clinvar
4
clinvar
74
clinvar
3
clinvar
 82
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 9 38 1698 824 8

Highest pathogenic variant AF is 0.000037982427

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAMD9protein_codingprotein_codingENST00000379958 118508
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
124725610081257390.00404
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7697097690.9220.000038410594
Missense in Polyphen173186.490.927672651
Synonymous0.07962772790.9940.00001412894
Loss of Function0.1045151.80.9840.00000288751

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.03630.0362
Ashkenazi Jewish0.000.00
East Asian0.002560.00256
Finnish0.0004640.000462
European (Non-Finnish)0.001780.00178
Middle Eastern0.002560.00256
South Asian0.003040.00304
Other0.002780.00277

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in the inflammatory response to tissue injury and the control of extra-osseous calcification, acting as a downstream target of TNF-alpha signaling. Involved in the regulation of EGR1, in coordination with RGL2. May be involved in endosome fusion. {ECO:0000269|PubMed:16960814, ECO:0000269|PubMed:18094730, ECO:0000269|PubMed:21160498, ECO:0000269|PubMed:24029230}.;
Disease
DISEASE: Tumoral calcinosis, normophosphatemic, familial (NFTC) [MIM:610455]: An uncommon, life-threatening disorder characterized by progressive deposition of calcified masses in cutaneous and subcutaneous tissues. Serum phosphate levels are normal. Clinical features include painful calcified ulcerative lesions and massive calcium deposition in the mid- and lower dermis, severe skin and bone infections, erythematous papular skin eruption in infancy, conjunctivitis, and gingivitis. NFTC shows a striking resemblance to acquired dystrophic calcinosis, in which tissue calcification occurs as a consequence of tissue injury/inflammation. {ECO:0000269|PubMed:16960814, ECO:0000269|PubMed:18094730}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: MIRAGE syndrome (MIRAGE) [MIM:617053]: A form of syndromic adrenal hypoplasia characterized by myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital phenotypes, and enteropathy. {ECO:0000269|PubMed:27182967}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.0928

Intolerance Scores

loftool
0.991
rvis_EVS
1.12
rvis_percentile_EVS
92.11

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.258

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
endosomal vesicle fusion
Cellular component
cytoplasm;cytosol;intracellular membrane-bounded organelle
Molecular function
protein binding
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