SMC2

protein-coding

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

Gene summary

Predicted to enable chromatin binding activity. Involved in mitotic chromosome condensation and positive regulation of chromosome condensation. Located in condensed chromosome; cytoplasm; and nuclear lumen. Part of condensin complex. Implicated in colon adenocarcinoma. Biomarker of colorectal cancer. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SMC2L1

MANE transcript

NM_006444.3

Inheritance

—

ClinVar variants

U:162B:9

Top phenotype

Wiedemann-Rautenstrauch-like progeroid syndrome

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr9:104,094,260-104,141,419

External References & Databases

Ensembl (ENSG00000136824)

Transcript & Mutation Effects

hg38 • Region Span ~47.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SMC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 153

not providedTotal: 9

Wiedemann-Rautenstrauch-like progeroid syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006444.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		1 clinvar	3
missense			155 clinvar	4 clinvar	4 clinvar	163
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	162	4	5	171

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006444.3	RefSeq	NP_006435.2	24	MANE Select
ENST00000374793.8	Ensembl	ENSP00000363925.3	24	MANE Select
NM_001042550.2	RefSeq	NP_001036015.1	24	Standard
NM_001042551.2	RefSeq	NP_001036016.1	24	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinoblastoma (RB) in Cancer
Condensation of Prophase Chromosomes
Mitotic Prophase
Condensation of Prometaphase Chromosomes
Mitotic Prometaphase

Biological Process

mitotic chromosome condensation
meiotic chromosome condensation
meiotic chromosome segregation
cell division
kinetochore organization

Molecular Function

single-stranded DNA binding
protein binding
ATP binding
protein heterodimerization activity

Cellular Component

nuclear chromosome
condensed chromosome
condensin complex
nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286398
Coding exons: 24
Length: 47158
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125743
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	517	589	0.877	0.0000284	7918
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00035	0.00033	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00021	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.387

Intolerance Scores

LoFtool: 0.175
RVIS EVS: -0.64
RVIS percentile EVS: 16.74

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.543

Gene Damage Prediction

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