SAMD1

sterile alpha motif domain containing 1, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 19:14087851-14091036

Links

ENSG00000141858 ∙ NCBI:90378 ∙ OMIM:620206 ∙ HGNC:17958 ∙ Uniprot:Q6SPF0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD1 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				3		3
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	0

Variants in SAMD1

This is a list of pathogenic ClinVar variants found in the SAMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14089932-G-A			Likely benign (Jun 01, 2023)
19-14090076-T-G			Likely benign (Aug 01, 2024)
19-14090079-C-G			Likely benign (Apr 01, 2024)
19-14090322-C-G		not specified	Uncertain significance (Feb 03, 2022)
19-14090332-T-C		not specified	Uncertain significance (Feb 07, 2025)
19-14090335-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-14090338-G-T		not specified	Uncertain significance (Mar 28, 2023)
19-14090344-G-A		not specified	Uncertain significance (Oct 08, 2024)
19-14090357-C-T		not specified	Uncertain significance (Apr 07, 2023)
19-14090369-T-G		not specified	Uncertain significance (Oct 01, 2024)
19-14090371-G-C		not specified	Uncertain significance (Feb 27, 2024)
19-14090372-T-G		not specified	Uncertain significance (Jan 24, 2023)
19-14090383-G-C		not specified	Uncertain significance (Mar 26, 2024)
19-14090404-G-C		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD1	protein_coding	protein_coding	ENST00000533683	5	3197

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.236	0.758	124596	0	8	124604	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0575	159	161	0.987	0.0000102	2672
Missense in Polyphen		32	58.291	0.54897		574
Synonymous	-3.16	102	68.7	1.48	0.00000469	936
Loss of Function	2.35	3	11.7	0.257	6.59e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000448	0.0000443
Middle Eastern	0.00	0.00
South Asian	0.0000657	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in atherogenesis by immobilizing LDL in the atherial wall. {ECO:0000269|PubMed:16159594}.

Recessive Scores

• pRec: 0.126

Haploinsufficiency Scores

• pHI: 0.414
• hipred: N
• hipred_score: 0.199
• ghis: 0.530

Essentials

• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Samd1

Gene ontology

• Cellular component: extracellular region;cytoplasm