SMC2

structural maintenance of chromosomes 2, the group of Condensin I subunits|Condensin II subunits|Structural maintenance of chromosomes proteins

Basic information

Region (hg38): 9:104094259-104141419

Previous symbols: [ "SMC2L1" ]

Links

ENSG00000136824 ∙ NCBI:10592 ∙ OMIM:605576 ∙ HGNC:14011 ∙ Uniprot:O95347 ∙ 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 SMC2 gene.

• Inborn genetic diseases (55 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMC2 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
missense			53	3	4	60
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	55	3	5

Variants in SMC2

This is a list of pathogenic ClinVar variants found in the SMC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-104095434-G-A		not specified	Uncertain significance (Sep 30, 2021)
9-104095467-A-G		not specified	Uncertain significance (Jun 10, 2022)
9-104096272-A-C		not specified	Uncertain significance (Feb 07, 2023)
9-104098498-A-C			Likely benign (Aug 03, 2017)
9-104100107-A-G		not specified	Uncertain significance (Jan 22, 2024)
9-104100147-A-G		not specified	Uncertain significance (Aug 12, 2021)
9-104100202-C-T		not specified	Uncertain significance (Sep 28, 2022)
9-104101961-A-G		not specified	Uncertain significance (Jul 14, 2023)
9-104101967-C-G		not specified	Uncertain significance (Feb 07, 2023)
9-104102017-C-T		not specified	Uncertain significance (Apr 06, 2023)
9-104102029-G-T		not specified	Uncertain significance (Mar 06, 2023)
9-104102043-G-T		not specified	Uncertain significance (Feb 14, 2023)
9-104102050-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-104102066-G-A		not specified	Uncertain significance (Nov 27, 2023)
9-104102126-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-104102152-C-T			Benign (Dec 31, 2019)
9-104102427-A-C		not specified	Uncertain significance (Jun 28, 2022)
9-104102442-C-T			Uncertain significance (Oct 11, 2023)
9-104102499-G-A		not specified	Uncertain significance (Jun 12, 2023)
9-104102499-G-T		not specified	Uncertain significance (Jun 30, 2023)
9-104102526-G-A			Benign (Jul 23, 2018)
9-104111667-T-C			Benign (Dec 31, 2019)
9-104111669-C-T		not specified	Uncertain significance (Apr 19, 2023)
9-104111713-G-T		not specified	Uncertain significance (Apr 25, 2022)
9-104111759-G-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMC2	protein_coding	protein_coding	ENST00000286398	24	47158

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000102	125714	0	29	125743	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	517	589	0.877	0.0000284	7918
Missense in Polyphen		85	155.81	0.54553		2139
Synonymous	-0.486	209	200	1.04	0.00000935	2150
Loss of Function	6.32	8	61.4	0.130	0.00000323	813

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000346	0.000326
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000346	0.000326
South Asian	0.000214	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Central component of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes. The condensin complex probably introduces positive supercoils into relaxed DNA in the presence of type I topoisomerases and converts nicked DNA into positive knotted forms in the presence of type II topoisomerases. {ECO:0000269|PubMed:11136719}.
• Pathway: Retinoblastoma (RB) in Cancer;Condensation of Prophase Chromosomes;Mitotic Prophase;Condensation of Prometaphase Chromosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.387

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.74

Haploinsufficiency Scores

• pHI: 0.889
• hipred: Y
• hipred_score: 0.800
• ghis: 0.694

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smc2
• 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); 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); cellular phenotype

Gene ontology

• Biological process: mitotic chromosome condensation;meiotic chromosome condensation;meiotic chromosome segregation;cell division;kinetochore organization
• Cellular component: nuclear chromosome;condensed chromosome;condensin complex;nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;extracellular exosome
• Molecular function: single-stranded DNA binding;protein binding;ATP binding;protein heterodimerization activity