SAMD5

protein-coding

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

Gene summary

Predicted to be involved in regulation of intracellular signal transduction. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001030060.3

Inheritance

—

ClinVar variants

U:32

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr6:147,508,690-147,737,547

External References & Databases

Ensembl (ENSG00000203727)

Transcript & Mutation Effects

hg38 • Region Span ~228.9 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 SAMD5 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 32

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001030060.3. 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

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001030060.3	RefSeq	NP_001025231.1	2	MANE Select
ENST00000367474.2	Ensembl	ENSP00000356444.1	2	MANE Select
ENST00000566741.1	Ensembl	ENSP00000456528.1	2	Standard
ENST00001135076.1	Ensembl	ENSP00000809248.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of JUN kinase activity
positive regulation of NIK/NF-kappaB signaling

Molecular Function

mitogen-activated protein kinase kinase kinase binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367474
Coding exons: 2
Length: 228621
Individuals with no LoFs: 124458
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 124470
p: 0.0000482

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.423	74	85.0	0.871	0.00000399	1072
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000054	0.000054	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0991

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0956

Gene Damage Prediction

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