SAMD4B

protein-coding

sterile alpha motif domain containing 4B, the group of Sterile alpha motif domain containing|Armadillo like helical domain containing

Gene summary

Enables RNA binding activity. Predicted to be involved in nuclear-transcribed mRNA poly(A) tail shortening. Predicted to act upstream of or within cerebellar neuron development. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001384574.2

Inheritance

—

ClinVar variants

U:90B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr19:39,342,421-39,385,710

External References & Databases

Ensembl (ENSG00000179134)

Transcript & Mutation Effects

hg38 • Region Span ~43.3 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 SAMD4B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001384574.2. 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			1 clinvar			1
missense			83 clinvar	1 clinvar		84
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	90	1	0	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001384574.2	RefSeq	NP_001371503.1	12	MANE Select
ENST00000610417.5	Ensembl	ENSP00000484229.1	12	MANE Select
NM_001303614.2	RefSeq	NP_001290543.1	12	Standard
NM_001384565.1	RefSeq	NP_001371494.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nuclear-transcribed mRNA poly(A) tail shortening
negative regulation of translation
regulation of mRNA stability

Molecular Function

RNA binding
mRNA binding
translation repressor activity

Cellular Component

P-body
nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000314471
Coding exons: 12
Length: 43315
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125740
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.04	254	432	0.588	0.0000274	4451
Missense (PolyPhen)		33	116.68	0.28283		1242
Synonymous	0.394	175	182	0.963	0.0000117	1477
Loss of Function	5.18	1	33.2	0.0302	0.00000175	336

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has transcriptional repressor activity. Overexpression inhibits the transcriptional activities of AP-1, p53/TP53 and CDKN1A. {ECO:0000269|PubMed:20510020}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

RVIS EVS: -0.91
RVIS percentile EVS: 9.9

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.860

Gene Damage Prediction

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