SAMD4A

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

Basic information

Region (hg38): 14:54566116-54793315

Previous symbols: [ "SAMD4" ]

Links

ENSG00000020577 ∙ NCBI:23034 ∙ OMIM:610747 ∙ HGNC:23023 ∙ Uniprot:Q9UPU9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD4A gene.

• Inborn genetic diseases (9 variants)
• not provided (4 variants)
• Lip and oral cavity carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD4A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	9	1	1

Variants in SAMD4A

This is a list of pathogenic ClinVar variants found in the SAMD4A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-54568053-A-G		not specified	Uncertain significance (Jun 09, 2022)
14-54568108-C-G		not specified	Uncertain significance (Aug 08, 2022)
14-54568111-C-T			Benign (Feb 13, 2018)
14-54702356-G-C		not specified	Uncertain significance (Dec 27, 2022)
14-54702428-A-G			Uncertain significance (-)
14-54702568-A-C		not specified	Uncertain significance (Jan 03, 2024)
14-54737254-A-G		not specified	Uncertain significance (Jan 18, 2022)
14-54751453-T-A		not specified	Uncertain significance (Mar 07, 2024)
14-54755757-T-C		Lip and oral cavity carcinoma	association (-)
14-54760222-C-T		not specified	Uncertain significance (Nov 17, 2022)
14-54760243-C-T		not specified	Uncertain significance (May 17, 2023)
14-54760252-C-G		not specified	Uncertain significance (Oct 10, 2023)
14-54760290-C-G		not specified	Uncertain significance (Jan 07, 2022)
14-54760372-C-T		not specified	Uncertain significance (Sep 16, 2021)
14-54764449-T-C			Benign (Feb 13, 2018)
14-54764515-T-C		not specified	Uncertain significance (Aug 17, 2022)
14-54774964-G-A			Benign (Apr 10, 2018)
14-54776457-G-A		not specified	Uncertain significance (Jun 03, 2022)
14-54776518-C-T			Benign/Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD4A	protein_coding	protein_coding	ENST00000392067	12	226219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000421	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.84	310	416	0.746	0.0000255	4650
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000333	0.0000333
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000652	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000805	0.0000791
Middle Eastern	0.0000652	0.0000544
South Asian	0.000102	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.899
• hipred: Y
• hipred_score: 0.661
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd4
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;negative regulation of translation;regulation of mRNA stability;positive regulation of translation
• Cellular component: P-body;fibrillar center;cytosol;cell junction;dendrite;synapse
• Molecular function: RNA binding;mRNA binding;protein binding;translation repressor activity