SAMD10

sterile alpha motif domain containing 10, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 20:63974116-63980008

Previous symbols: [ "C20orf136" ]

Links

ENSG00000130590 ∙ NCBI:140700 ∙ ∙ HGNC:16129 ∙ Uniprot:Q9BYL1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_080621.5	NP_542188.1	5	yes	-
ENST00000369886.8	ENSP00000358902.3	5	yes	-
ENST00000450107.1	ENSP00000404839.1	3	-	-
XM_005260199.5	XP_005260256.1	6	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD10 gene.

• not_specified (31 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_080621.5. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			32			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD10	protein_coding	protein_coding	ENST00000369886	5	5896

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125720	0	7	125727	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.790	95	119	0.796	0.00000800	1280
Missense in Polyphen		25	39.864	0.62713		430
Synonymous	-0.279	54	51.5	1.05	0.00000315	423
Loss of Function	0.970	6	9.17	0.654	3.94e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000319	0.0000319
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.359
• rvis_EVS: 0.28
• rvis_percentile_EVS: 71.27

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.445

Gene Damage Prediction

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