SAMD1

protein-coding

sterile alpha motif domain containing 1, the group of Sterile alpha motif domain containing

Gene summary

Enables chromatin binding activity. Involved in negative regulation of transcription initiation-coupled chromatin remodeling and protein homooligomerization. Is active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:10B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr19:14,087,851-14,091,036

External References & Databases

Ensembl (ENSG00000141858)

Transcript & Mutation Effects

hg38 • Region Span ~3.2 kb

Loading mutation effect viewer...

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 SAMD1 variants in ClinVar

0 Conditions Cataloged

No annotated ClinVar phenotypes.

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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				3 clinvar		3
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	3	0	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138352.3	RefSeq	NP_612361.1	5	Standard
ENST00000269724.5	Ensembl	ENSP00000269724.5	4	Standard
ENST00000533683.7	Ensembl	ENSP00000431971.2	5	Standard
ENST00000533683.8	Ensembl	ENSP00000431971.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000533683
Coding exons: 5
Length: 3197
Individuals with no LoFs: 124596
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124604
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0575	159	161	0.987	0.0000102	2672
Missense (PolyPhen)		32	58.291	0.54897		574
Synonymous	-3.16	102	68.7	1.48	0.00000469	936
Loss of Function	2.35	3	11.7	0.257	6.59e-7	163

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	0.000046	0.000046	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in atherogenesis by immobilizing LDL in the atherial wall. {ECO:0000269|PubMed:16159594}.;

Recessive Scores

pRec: 0.126

Essentials

Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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