SMC1B

structural maintenance of chromosomes 1B, the group of Structural maintenance of chromosomes proteins|Cohesin complex

Basic information

Region (hg38): 22:45344063-45413619

Previous symbols: [ "SMC1L2" ]

Links

ENSG00000077935 ∙ NCBI:27127 ∙ OMIM:608685 ∙ HGNC:11112 ∙ Uniprot:Q8NDV3 ∙ 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 SMC1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMC1B 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	3	4
missense			40	2	2	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding					1	1
Total	0	0	40	3	6

Variants in SMC1B

This is a list of pathogenic ClinVar variants found in the SMC1B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-45344560-C-T		not specified	Likely benign (May 31, 2022)
22-45344581-C-G			Benign (Jul 17, 2018)
22-45345464-G-C		not specified	Uncertain significance (Jun 11, 2021)
22-45345483-G-A			Benign (Jul 16, 2018)
22-45345485-C-T		not specified	Uncertain significance (Mar 31, 2023)
22-45349748-C-G		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
22-45352546-G-T		not specified	Uncertain significance (Mar 30, 2022)
22-45352609-C-T			Likely benign (Dec 31, 2019)
22-45354031-A-G		not specified	Uncertain significance (Oct 16, 2023)
22-45354086-G-C			Benign (Apr 19, 2019)
22-45358749-T-C		not specified	Uncertain significance (Mar 21, 2023)
22-45358755-A-G		not specified	Uncertain significance (Dec 02, 2024)
22-45359818-A-G		not specified	Uncertain significance (Jan 03, 2022)
22-45359899-C-T		not specified	Uncertain significance (Feb 28, 2023)
22-45359911-A-T		not specified	Uncertain significance (Aug 10, 2024)
22-45359924-T-C		not specified	Uncertain significance (Sep 24, 2024)
22-45359968-C-T			Benign (Jul 16, 2018)
22-45362973-C-T		not specified	Uncertain significance (May 12, 2024)
22-45369965-A-C		not specified	Uncertain significance (Apr 09, 2024)
22-45369979-G-A		not specified	Uncertain significance (Nov 29, 2024)
22-45369990-T-G		not specified	Uncertain significance (Feb 23, 2023)
22-45371505-C-T		not specified	Likely benign (Jun 03, 2024)
22-45371533-A-G			Benign (Dec 31, 2019)
22-45371587-C-T		not specified	Uncertain significance (Jun 07, 2024)
22-45372190-T-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMC1B	protein_coding	protein_coding	ENST00000357450	25	69557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.104	0.896	124760	0	34	124794	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	486	623	0.781	0.0000316	8194
Missense in Polyphen		132	208.99	0.63161		2798
Synonymous	0.970	198	216	0.916	0.0000109	2143
Loss of Function	5.92	17	70.8	0.240	0.00000389	884

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000131	0.000131
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.0000583	0.0000556
Finnish	0.0000931	0.0000928
European (Non-Finnish)	0.000208	0.000203
Middle Eastern	0.0000583	0.0000556
South Asian	0.0000683	0.0000654
Other	0.000168	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Meiosis-specific component of cohesin complex. Required for the maintenance of meiotic cohesion, but not, or only to a minor extent, for its establishment. Contributes to axial element (AE) formation and the organization of chromatin loops along the AE. Plays a key role in synapsis, recombination and chromosome movements. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The meiosis-specific cohesin complex probably replaces mitosis specific cohesin complex when it dissociates from chromatin during prophase I (By similarity). {ECO:0000250}.
• Pathway: Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Reproduction;Meiotic synapsis;Meiosis;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.0847

Intolerance Scores

• loftool: 0.366
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.73

Haploinsufficiency Scores

• pHI: 0.513
• hipred: Y
• hipred_score: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smc1b
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; normal phenotype; reproductive system phenotype

Gene ontology

• Biological process: sister chromatid cohesion;meiotic cell cycle
• Cellular component: chromosome, centromeric region;lateral element;nucleoplasm;cytosol;meiotic cohesin complex;nuclear meiotic cohesin complex
• Molecular function: DNA binding;ATP binding