SAMD10

protein-coding

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

Gene summary

Predicted to be involved in cell surface receptor protein tyrosine kinase signaling pathway. Predicted to be active in cytoplasmic side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf136

MANE transcript

NM_080621.5

Inheritance

—

ClinVar variants

U:32

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr20:63,974,116-63,980,008

External References & Databases

Ensembl (ENSG00000130590)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAMD10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_080621.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	0	0	32

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_080621.5	RefSeq	NP_542188.1	5	MANE Select
ENST00000369886.8	Ensembl	ENSP00000358902.3	5	MANE Select
ENST00000450107.1	Ensembl	ENSP00000404839.1	3	Standard
ENST00000979707.1	Ensembl	ENSP00000649524.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369886
Coding exons: 5
Length: 5896
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125727
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.790	95	119	0.796	0.00000800	1280
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.359
RVIS EVS: 0.28
RVIS percentile EVS: 71.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.445

Gene Damage Prediction

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