SAMD9L

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

Basic information

Region (hg38): 7:93130055-93148385

Previous symbols: [ "C7orf6" ]

Links

ENSG00000177409 ∙ NCBI:219285 ∙ OMIM:611170 ∙ HGNC:1349 ∙ Uniprot:Q8IVG5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the SAMD9L gene.

• not provided (669 variants)
• not specified (74 variants)
• Inborn genetic diseases (35 variants)
• Ataxia-pancytopenia syndrome (30 variants)
• SAMD9L-related condition (24 variants)
• Monosomy 7 myelodysplasia and leukemia syndrome 1 (9 variants)
• Ataxia-pancytopenia syndrome;Monosomy 7 myelodysplasia and leukemia syndrome 1;Spinocerebellar ataxia 49 (3 variants)
• Monosomy 7 myelodysplasia and leukemia syndrome 1;Ataxia-pancytopenia syndrome;Spinocerebellar ataxia 49 (3 variants)
• Spinocerebellar ataxia 49 (3 variants)
• Microcephaly (2 variants)
• Spinocerebellar ataxia 49;Monosomy 7 myelodysplasia and leukemia syndrome 1;Ataxia-pancytopenia syndrome (2 variants)
• Monosomy 7 myelodysplasia and leukemia syndrome 1;Ataxia-pancytopenia syndrome (1 variants)
• See cases (1 variants)
• Intellectual disability (1 variants)
• Ataxia-pancytopenia syndrome;Spinocerebellar ataxia 49;Monosomy 7 myelodysplasia and leukemia syndrome 1 (1 variants)
• Monosomy 7 myelodysplasia and leukemia syndrome 1;Spinocerebellar ataxia 49;Ataxia-pancytopenia syndrome (1 variants)
• SAMD9L-Related Disorders (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.

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			8	160	7	175
missense	3	6	446	11	13	479
nonsense			31			31
start loss			1			1
frameshift		2	26	1		29
inframe indel			5			5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	1	3
Total	3	8	518	173	21

Variants in SAMD9L

This is a list of pathogenic ClinVar variants found in the SAMD9L region.

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

Position	Type	Phenotype	Significance	ClinVar
7-93131118-G-A			Likely benign (Jun 15, 2019)
7-93131236-T-C		not specified	Uncertain significance (Sep 05, 2022)
7-93131238-T-C			Likely benign (Sep 27, 2023)
7-93131254-A-G		not specified • Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
7-93131254-A-T			Conflicting classifications of pathogenicity (Dec 06, 2023)
7-93131264-C-A			Uncertain significance (Jul 19, 2022)
7-93131279-CTCTT-C			Uncertain significance (May 11, 2022)
7-93131293-C-A			Uncertain significance (Aug 24, 2023)
7-93131295-A-G			Likely benign (Apr 23, 2022)
7-93131304-G-A			Likely benign (Dec 14, 2023)
7-93131307-T-A			Likely benign (Feb 05, 2022)
7-93131311-C-G		SAMD9L-related disorder	Uncertain significance (Mar 25, 2023)
7-93131318-A-T		Monosomy 7 myelodysplasia and leukemia syndrome 1	Likely pathogenic (Nov 04, 2021)
7-93131326-A-G			Uncertain significance (May 16, 2021)
7-93131330-C-T			Uncertain significance (Oct 13, 2023)
7-93131343-T-C			Likely benign (Oct 17, 2023)
7-93131343-T-G			Uncertain significance (Jan 31, 2023)
7-93131348-C-T			Uncertain significance (Jan 24, 2023)
7-93131351-C-G			Uncertain significance (Jul 06, 2022)
7-93131356-C-T			Uncertain significance (May 01, 2022)
7-93131358-A-G			Likely benign (Jan 27, 2024)
7-93131359-T-C			Uncertain significance (Aug 31, 2022)
7-93131365-A-G			Uncertain significance (Aug 13, 2022)
7-93131373-T-C		SAMD9L-related disorder	Likely benign (Nov 01, 2022)
7-93131384-C-T			Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

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: 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

• 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