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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	23	0	0

Variants in SAMD10

This is a list of pathogenic ClinVar variants found in the SAMD10 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63975517-A-G		not specified	Uncertain significance (Nov 30, 2022)
20-63975727-C-T		not specified	Uncertain significance (Nov 14, 2024)
20-63975815-G-C		not specified	Uncertain significance (Sep 22, 2023)
20-63977007-C-T		not specified	Uncertain significance (Oct 13, 2023)
20-63977016-T-A		not specified	Uncertain significance (Apr 04, 2024)
20-63977043-T-G		not specified	Uncertain significance (Feb 15, 2023)
20-63977079-G-A		not specified	Uncertain significance (Jan 17, 2023)
20-63977088-C-A		not specified	Uncertain significance (Jan 23, 2024)
20-63977138-C-T		not specified	Uncertain significance (Jul 06, 2021)
20-63977139-G-A		not specified	Uncertain significance (Feb 17, 2024)
20-63977141-C-T		not specified	Uncertain significance (Dec 16, 2022)
20-63977280-G-A		not specified	Uncertain significance (Nov 27, 2024)
20-63977281-C-T		not specified	Uncertain significance (Dec 10, 2024)
20-63977283-C-T		not specified	Uncertain significance (May 24, 2023)
20-63977292-C-T		not specified	Uncertain significance (May 13, 2022)
20-63977303-C-G		not specified	Uncertain significance (Feb 04, 2025)
20-63977323-G-A		not specified	Uncertain significance (Sep 10, 2024)
20-63977364-G-A		not specified	Uncertain significance (Sep 10, 2024)
20-63977368-G-C		not specified	Uncertain significance (Feb 07, 2025)
20-63977377-G-A		not specified	Uncertain significance (Jun 30, 2022)
20-63977377-G-C		not specified	Uncertain significance (Oct 11, 2024)
20-63977383-G-A		not specified	Uncertain significance (Jun 21, 2023)
20-63977410-T-C			Likely benign (Jul 11, 2023)
20-63979388-C-G		not specified	Uncertain significance (Nov 21, 2022)
20-63979391-C-T		not specified	Uncertain significance (Sep 01, 2021)

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
0.000659	0.755	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

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.346
• ghis: 0.481

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

Mouse Genome Informatics

• Gene name: Samd10