SMARCD3

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 3, the group of BAF complex|GBAF complex|PBAF complex

Basic information

Region (hg38): 7:151238764-151277896

Links

ENSG00000082014

∙ NCBI:6604 ∙ OMIM:601737 ∙ HGNC:11108 ∙ Uniprot:Q6STE5 ∙ 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 SMARCD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMARCD3 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			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in SMARCD3

This is a list of pathogenic ClinVar variants found in the SMARCD3 region.

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

Position	Phenotype	Significance	ClinVar
7-151239464-C-T	not specified	Uncertain significance (Oct 17, 2023)	3166349
7-151239479-C-T	not specified	Uncertain significance (Jun 29, 2022)	2386830
7-151239482-C-A	not specified	Uncertain significance (Nov 09, 2024)	3446129
7-151239647-G-A	not specified	Uncertain significance (Sep 26, 2023)	3166348
7-151239667-C-G	not specified	Uncertain significance (Aug 30, 2022)	2387133
7-151239692-G-T	not specified	Uncertain significance (May 09, 2024)	3320842
7-151240126-C-T	not specified	Uncertain significance (Jul 09, 2024)	3446131
7-151240141-G-C	not specified	Uncertain significance (Apr 12, 2024)	3320841
7-151240444-C-T	not specified	Uncertain significance (Sep 20, 2023)	3166347
7-151240479-C-T	not specified	Uncertain significance (Feb 03, 2022)	2377970
7-151240494-G-A	not specified	Uncertain significance (Jul 14, 2024)	3446132
7-151240506-C-T	not specified	Uncertain significance (Nov 14, 2023)	3166350
7-151241902-G-A	not specified	Uncertain significance (Jan 19, 2022)	2272276
7-151242531-C-T	not specified	Uncertain significance (Jul 11, 2023)	2601153
7-151242597-G-A	not specified	Uncertain significance (Nov 08, 2021)	2259266
7-151242809-A-G	not specified	Uncertain significance (May 24, 2023)	2551713
7-151243671-G-C	not specified	Uncertain significance (Oct 06, 2024)	3446130
7-151243699-G-A	not specified	Uncertain significance (Apr 08, 2024)	3320840
7-151245523-G-A	not specified	Uncertain significance (Jul 07, 2022)	2206242
7-151245566-G-A	not specified	Uncertain significance (Dec 01, 2022)	2405636
7-151245598-A-T		Uncertain significance (May 01, 2022)	2658188
7-151248493-G-A		Uncertain significance (May 01, 2022)	2658189

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMARCD3	protein_coding	protein_coding	ENST00000262188	13	39133

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.405	0.595	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.58	139	255	0.546	0.0000158	3166
Missense in Polyphen		46	90.279	0.50953		949
Synonymous	-0.404	106	101	1.05	0.00000574	946
Loss of Function	3.43	5	22.6	0.222	0.00000100	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000816	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000816	0.000816
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Stimulates nuclear receptor mediated transcription. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron- specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). {ECO:0000250|UniProtKB:Q6P9Z1, ECO:0000269|PubMed:29374058, ECO:0000269|PubMed:8804307, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.;
Pathway: Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Androgen Receptor Network in Prostate Cancer;Tumor suppressor activity of SMARCB1;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;Metabolism;Validated transcriptional targets of TAp63 isoforms;Chromatin organization;Transcriptional regulation by RUNX1;LKB1 signaling events (Consensus)

Recessive Scores

pRec: 0.186

Intolerance Scores

loftool: 0.555
rvis_EVS: -0.49
rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

pHI: 0.950
hipred: Y
hipred_score: 0.829
ghis: 0.638

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Smarcd3
Phenotype

Zebrafish Information Network

Gene name: smarcd3b
Affected structure: heart
Phenotype tag: abnormal
Phenotype quality: inverted

Gene ontology

Biological process: positive regulation of neuroblast proliferation;secondary heart field specification;cardiac right ventricle formation;neural retina development;nucleosome disassembly;chromatin remodeling;transcription, DNA-templated;regulation of transcription by RNA polymerase II;positive regulation of G2/M transition of mitotic cell cycle;regulation of lipid metabolic process;muscle cell differentiation;regulation of protein binding;positive regulation of transcription, DNA-templated;positive regulation of smooth muscle cell differentiation
Cellular component: nuclear chromatin;nucleus;nucleoplasm;SWI/SNF complex;npBAF complex;nBAF complex
Molecular function: chromatin binding;transcription coactivator activity;signaling receptor binding;transcription factor binding;nuclear hormone receptor binding