SAMD4B

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

Basic information

Region (hg38): 19:39342421-39385710

Links

ENSG00000179134 ∙ NCBI:55095 ∙ OMIM:619231 ∙ HGNC:25492 ∙ Uniprot:Q5PRF9 ∙ 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 SAMD4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD4B 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						0
missense			35			35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	0	0

Variants in SAMD4B

This is a list of pathogenic ClinVar variants found in the SAMD4B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-39369660-G-A		not specified	Uncertain significance (Nov 09, 2021)
19-39369798-G-A		not specified	Uncertain significance (Oct 12, 2021)
19-39369934-G-A		not specified	Uncertain significance (Oct 12, 2022)
19-39369936-T-G		not specified	Uncertain significance (Sep 14, 2022)
19-39369943-C-G		not specified	Uncertain significance (Dec 07, 2021)
19-39369943-C-T		not specified	Uncertain significance (Apr 19, 2024)
19-39369958-A-T		not specified	Uncertain significance (Dec 15, 2023)
19-39369963-C-T		not specified	Uncertain significance (Apr 12, 2022)
19-39369982-G-C		not specified	Uncertain significance (Sep 21, 2023)
19-39369982-G-T		not specified	Uncertain significance (Apr 08, 2024)
19-39370000-T-C		not specified	Uncertain significance (Oct 19, 2021)
19-39370008-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-39370044-C-T		not specified	Uncertain significance (Jun 26, 2023)
19-39370075-C-G		not specified	Uncertain significance (Nov 09, 2023)
19-39370077-A-G		not specified	Uncertain significance (Dec 03, 2021)
19-39370087-C-T		not specified	Uncertain significance (Mar 11, 2022)
19-39375686-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-39375734-C-T		not specified	Uncertain significance (Apr 28, 2022)
19-39375740-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-39375758-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-39375760-G-C		not specified	Uncertain significance (Jul 11, 2023)
19-39375818-C-G		not specified	Uncertain significance (Dec 15, 2023)
19-39376534-C-A		not specified	Uncertain significance (Sep 27, 2022)
19-39377486-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-39377581-G-A		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD4B	protein_coding	protein_coding	ENST00000314471	12	43315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000382	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.04	254	432	0.588	0.0000274	4451
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000890	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.182
• hipred: Y
• hipred_score: 0.662
• ghis: 0.662

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd4b

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;negative regulation of translation;regulation of mRNA stability
• Cellular component: P-body;nucleus;cytosol
• Molecular function: RNA binding;mRNA binding;translation repressor activity