SAMD4A

protein-coding

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

Gene summary

Sterile alpha motifs (SAMs) in proteins such as SAMD4A are part of an RNA-binding domain that functions as a posttranscriptional regulator by binding to an RNA sequence motif known as the Smaug recognition element, which was named after the Drosophila Smaug protein (Baez and Boccaccio, 2005 [PubMed 16221671]).[supplied by OMIM, Mar 2008]

Previous symbols:

SAMD4

MANE transcript

NM_015589.6

Inheritance

—

ClinVar variants

U:44B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr14:54,566,117-54,793,315

External References & Databases

Ensembl (ENSG00000020577)

Transcript & Mutation Effects

hg38 • Region Span ~227.2 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 SAMD4A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015589.6. 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 clinvar	2 clinvar	8
missense			39 clinvar			39
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	3	2	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015589.6	RefSeq	NP_056404.4	12	MANE Select
ENST00000554335.6	Ensembl	ENSP00000452535.1	12	MANE Select
NM_001161576.2	RefSeq	NP_001155048.2	11	Standard
NM_001161577.2	RefSeq	NP_001155049.1	8	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
positive regulation of translation

Molecular Function

RNA binding
mRNA binding
protein binding
translation repressor activity

Cellular Component

P-body
fibrillar center
cytosol
cell junction
dendrite

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000392067
Coding exons: 12
Length: 226219
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.84	310	416	0.746	0.0000255	4650
Missense (PolyPhen)		79	136.84	0.5773		1490
Synonymous	-0.420	175	168	1.04	0.0000105	1432
Loss of Function	5.06	3	35.6	0.0844	0.00000196	371

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000033	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000065	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.00010	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a translational repressor of SRE-containing messengers. {ECO:0000269|PubMed:16221671}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.143
RVIS EVS: -0.64
RVIS percentile EVS: 16.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.907

Gene Damage Prediction

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