SMC4

structural maintenance of chromosomes 4, the group of Structural maintenance of chromosomes proteins|Condensin I subunits|Condensin II subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:160399274-160434954

Previous symbols: [ "SMC4L1" ]

Links

ENSG00000113810 ∙ NCBI:10051 ∙ OMIM:605575 ∙ HGNC:14013 ∙ Uniprot:Q9NTJ3 ∙ 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 SMC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMC4 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			72	3	1	76
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding						0
Total	0	0	73	4	1

Variants in SMC4

This is a list of pathogenic ClinVar variants found in the SMC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-160399282-G-A		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399342-C-T		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399395-C-T		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399420-T-C		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399475-C-G		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399491-A-C		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160399509-C-A		Jeune thoracic dystrophy	Uncertain significance (Jun 14, 2016)
3-160400854-A-G		not specified	Uncertain significance (Feb 21, 2025)
3-160400855-C-T		not specified	Uncertain significance (Nov 14, 2023)
3-160400884-C-T		not specified	Uncertain significance (Jun 05, 2023)
3-160400894-C-G		not specified	Uncertain significance (Feb 07, 2025)
3-160400894-C-T		not specified	Uncertain significance (Nov 26, 2024)
3-160400914-G-A		not specified	Likely benign (Nov 23, 2022)
3-160400947-A-G		not specified	Uncertain significance (Aug 12, 2024)
3-160401978-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-160402059-A-G		not specified	Uncertain significance (Nov 25, 2024)
3-160402085-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-160402676-C-T		not specified	Uncertain significance (Nov 26, 2024)
3-160402811-C-T		not specified	Uncertain significance (Feb 19, 2025)
3-160402813-C-G		not specified	Uncertain significance (Apr 01, 2024)
3-160404346-G-A		not specified	Uncertain significance (Oct 09, 2024)
3-160404407-A-G		not specified	Uncertain significance (Aug 08, 2023)
3-160404439-G-T		not specified	Uncertain significance (Sep 11, 2024)
3-160404482-A-G		not specified	Uncertain significance (Sep 01, 2021)
3-160411920-G-A		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMC4	protein_coding	protein_coding	ENST00000357388	23	35689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000168	1.00	125600	0	147	125747	0.000585

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	574	652	0.881	0.0000332	8566
Missense in Polyphen		109	163.93	0.66492		2116
Synonymous	-1.60	248	218	1.14	0.0000114	2257
Loss of Function	4.81	20	60.3	0.331	0.00000297	853

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00107
Ashkenazi Jewish	0.000936	0.000794
East Asian	0.00143	0.00131
Finnish	0.000245	0.000185
European (Non-Finnish)	0.000594	0.000536
Middle Eastern	0.00143	0.00131
South Asian	0.000859	0.000784
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: 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: 0.276

Intolerance Scores

• loftool: 0.385
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.6

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.715
• ghis: 0.687

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smc4

Zebrafish Information Network

• Gene name: smc4
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

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