SAMD5

sterile alpha motif domain containing 5, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 6:147508690-147737547

Links

ENSG00000203727 ∙ NCBI:389432 ∙ ∙ HGNC:21180 ∙ Uniprot:Q5TGI4 ∙ 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 SAMD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD5 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in SAMD5

This is a list of pathogenic ClinVar variants found in the SAMD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-147508980-T-C		not specified	Uncertain significance (Sep 27, 2024)
6-147508986-G-C		not specified	Uncertain significance (Aug 11, 2024)
6-147509050-T-C		not specified	Uncertain significance (Dec 23, 2024)
6-147509140-G-T		not specified	Uncertain significance (Oct 22, 2021)
6-147509148-T-C		not specified	Uncertain significance (Nov 08, 2022)
6-147509160-C-A		not specified	Uncertain significance (Feb 27, 2023)
6-147509161-C-T		not specified	Uncertain significance (Jun 03, 2022)
6-147509197-T-G		not specified	Uncertain significance (Aug 17, 2021)
6-147509203-C-T		not specified	Uncertain significance (Feb 26, 2025)
6-147509208-C-T		not specified	Uncertain significance (May 16, 2022)
6-147509209-G-T		not specified	Uncertain significance (Sep 17, 2021)
6-147509229-G-C		not specified	Uncertain significance (Jan 14, 2025)
6-147509230-G-A		not specified	Uncertain significance (Mar 01, 2023)
6-147509286-A-G		not specified	Uncertain significance (May 13, 2024)
6-147509308-A-G		not specified	Uncertain significance (Nov 09, 2023)
6-147509321-G-T		not specified	Uncertain significance (Jun 11, 2021)
6-147509333-G-T		not specified	Uncertain significance (Aug 16, 2021)
6-147509358-C-T		not specified	Uncertain significance (Jan 21, 2025)
6-147509370-C-G		not specified	Uncertain significance (Feb 12, 2025)
6-147509371-C-T		not specified	Uncertain significance (Jun 21, 2022)
6-147509373-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-147509374-C-G		not specified	Uncertain significance (Sep 13, 2023)
6-147509385-A-G		not specified	Uncertain significance (Feb 13, 2025)
6-147564452-G-A		not specified	Uncertain significance (Aug 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD5	protein_coding	protein_coding	ENST00000367474	2	228621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0121	0.661	124458	0	12	124470	0.0000482

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	74	85.0	0.871	0.00000399	1072
Missense in Polyphen		28	43.6	0.6422		489
Synonymous	0.999	31	38.9	0.796	0.00000187	360
Loss of Function	0.496	3	4.08	0.735	1.75e-7	51

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	0.00	0.00
European (Non-Finnish)	0.0000539	0.0000539
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0991

Haploinsufficiency Scores

• pHI: 0.300
• hipred: N
• hipred_score: 0.412
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd5

Gene ontology

• Biological process: positive regulation of JUN kinase activity;positive regulation of NIK/NF-kappaB signaling
• Molecular function: mitogen-activated protein kinase kinase kinase binding