SMARCA1

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1, the group of Myb/SANT domain containing|NURF complex

Basic information

Region (hg38): X:129446501-129523500

Previous symbols: [ "SNF2L1", "SNF2L" ]

Links

ENSG00000102038 ∙ NCBI:6594 ∙ OMIM:300012 ∙ HGNC:11097 ∙ Uniprot:P28370 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: Unknown
• X-linked intellectual disability (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SMARCA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMARCA1 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				5	1	6
missense			33		3	36
nonsense		3	1			4
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1		3
non coding				1		1
Total	0	3	34	6	4

Variants in SMARCA1

This is a list of pathogenic ClinVar variants found in the SMARCA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-129448390-C-A		not specified	Uncertain significance (Aug 21, 2024)
X-129448392-T-C		not specified	Uncertain significance (May 30, 2024)
X-129448406-A-G		X-linked intellectual disability	Uncertain significance (Dec 21, 2022)
X-129448421-G-A		Inborn genetic diseases	Uncertain significance (Aug 25, 2017)
X-129465529-C-T			Likely benign (Feb 01, 2023)
X-129465608-C-T		not specified	Uncertain significance (Aug 10, 2021)
X-129465698-C-T		not specified	Uncertain significance (Sep 26, 2024)
X-129465875-C-T		not specified	Uncertain significance (Aug 27, 2024)
X-129468914-A-C			Likely benign (May 17, 2018)
X-129471205-T-C		not specified	Uncertain significance (Dec 03, 2024)
X-129471251-G-A		not specified	Uncertain significance (Dec 04, 2024)
X-129471259-C-G			Benign (Dec 31, 2019)
X-129471263-C-T		not specified	Uncertain significance (Nov 09, 2024)
X-129471267-C-G		not specified	Uncertain significance (Apr 09, 2024)
X-129471280-T-C		not specified	Uncertain significance (May 24, 2023)
X-129471289-G-C		not specified	Uncertain significance (Nov 29, 2024)
X-129480720-C-T		not specified	Uncertain significance (Jun 27, 2022)
X-129480734-T-C			Likely benign (May 16, 2018)
X-129480789-T-C			Uncertain significance (Feb 19, 2021)
X-129481079-G-T			Benign (Oct 23, 2018)
X-129481136-T-C		not specified	Uncertain significance (Aug 28, 2023)
X-129481149-C-T		not specified	Uncertain significance (Oct 20, 2024)
X-129487018-C-T		See cases	Uncertain significance (Jul 10, 2020)
X-129487074-C-T		not specified	Uncertain significance (Jul 22, 2021)
X-129487094-G-C		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMARCA1	protein_coding	protein_coding	ENST00000371122	24	76998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000161	124182	0	3	124185	0.0000121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.44	250	385	0.650	0.0000297	6949
Missense in Polyphen		59	147.19	0.40084		2574
Synonymous	0.785	115	126	0.911	0.00000891	1915
Loss of Function	6.01	2	46.0	0.0434	0.00000405	765

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000392	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Energy-transducing component of NURF (nucleosome- remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes. Both complexes facilitate the perturbation of chromatin structure in an ATP-dependent manner. Potentiates neurite outgrowth. May be involved in brain development by regulating En-1 and En-2 expression. May be involved in the development of luteal cells. {ECO:0000269|PubMed:14609955, ECO:0000269|PubMed:15310751, ECO:0000269|PubMed:15640247, ECO:0000269|PubMed:16740656}.
• Pathway: Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.0448
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.992
• hipred: Y
• hipred_score: 0.859
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.947

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smarca1
• Phenotype: growth/size/body region phenotype; cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype

Zebrafish Information Network

• Gene name: smarca1
• Affected structure: primitive erythrocyte differentiation
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: DNA strand renaturation;chromatin remodeling;brain development;neuron differentiation;ATP-dependent chromatin remodeling;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;NURF complex;intracellular membrane-bounded organelle;CERF complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;helicase activity;protein binding;ATP binding;DNA-dependent ATPase activity;transcription factor binding;nucleosome binding;annealing helicase activity;nucleosome-dependent ATPase activity