SAMD15

sterile alpha motif domain containing 15, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 14:77376689-77392163

Previous symbols: [ "FAM15A", "C14orf174" ]

Links

ENSG00000100583 ∙ NCBI:161394 ∙ ∙ HGNC:18631 ∙ Uniprot:Q9P1V8 ∙ 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 SAMD15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD15 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			27	5		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	5	0

Variants in SAMD15

This is a list of pathogenic ClinVar variants found in the SAMD15 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-77376957-C-A		not specified	Uncertain significance (May 24, 2023)
14-77377011-G-A		not specified	Uncertain significance (Nov 22, 2021)
14-77377050-A-C		not specified	Uncertain significance (Jun 21, 2021)
14-77377428-G-T		not specified	Uncertain significance (Apr 12, 2022)
14-77377447-C-G		not specified	Uncertain significance (Jun 29, 2022)
14-77377528-C-T		not specified	Uncertain significance (Nov 18, 2022)
14-77377530-G-A		not specified	Uncertain significance (Oct 25, 2023)
14-77377548-G-T		not specified	Uncertain significance (Apr 17, 2023)
14-77377552-C-T		not specified	Uncertain significance (Dec 26, 2023)
14-77377588-C-T		not specified	Uncertain significance (Dec 20, 2023)
14-77377639-A-T		not specified	Uncertain significance (Jan 03, 2024)
14-77377674-G-A		not specified	Uncertain significance (Dec 11, 2023)
14-77377704-C-T		not specified	Likely benign (May 27, 2022)
14-77377707-A-G		not specified	Uncertain significance (Dec 09, 2023)
14-77377770-T-G		not specified	Uncertain significance (Dec 11, 2023)
14-77377794-A-G		not specified	Likely benign (Mar 14, 2023)
14-77377942-C-G		not specified	Uncertain significance (Apr 13, 2022)
14-77378020-A-G		not specified	Uncertain significance (Jan 23, 2024)
14-77378130-C-T		not specified	Uncertain significance (May 06, 2022)
14-77378176-G-C		not specified	Uncertain significance (Jul 14, 2021)
14-77378211-C-A		not specified	Uncertain significance (Jun 24, 2022)
14-77378267-G-C		not specified	Uncertain significance (May 31, 2022)
14-77378283-C-G		not specified	Uncertain significance (Jan 02, 2024)
14-77378338-G-A		not specified	Likely benign (Sep 17, 2021)
14-77378354-T-G		not specified	Likely benign (Nov 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD15	protein_coding	protein_coding	ENST00000216471	3	14809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.24e-10	0.326	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	334	346	0.965	0.0000171	4424
Missense in Polyphen		36	43.686	0.82406		620
Synonymous	1.14	115	132	0.874	0.00000690	1260
Loss of Function	0.953	18	22.9	0.785	0.00000106	340

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.85
• rvis_percentile_EVS: 88.48

Haploinsufficiency Scores

• pHI: 0.0819
• hipred: N
• hipred_score: 0.123
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• 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: Samd15