NCAPG

non-SMC condensin I complex subunit G, the group of Condensin I subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 4:17810978-17844865

Links

ENSG00000109805 ∙ NCBI:64151 ∙ OMIM:606280 ∙ HGNC:24304 ∙ Uniprot:Q9BPX3 ∙ 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 NCAPG gene.

• Inborn genetic diseases (32 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAPG 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						0
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in NCAPG

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

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

Position	Type	Phenotype	Significance	ClinVar
4-17811151-C-T		not specified	Uncertain significance (Jan 26, 2022)
4-17811175-G-T		not specified	Uncertain significance (Dec 15, 2023)
4-17812314-A-G		not specified	Uncertain significance (Apr 13, 2022)
4-17812342-C-T		not specified	Uncertain significance (Jan 03, 2024)
4-17813020-T-A		not specified	Uncertain significance (Apr 04, 2023)
4-17813064-A-T		not specified	Uncertain significance (Jan 04, 2022)
4-17813092-T-C		not specified	Uncertain significance (Sep 13, 2023)
4-17813095-C-T		not specified	Uncertain significance (Aug 23, 2021)
4-17813130-T-C		not specified	Uncertain significance (Apr 04, 2023)
4-17814897-C-T		not specified	Uncertain significance (Jun 27, 2022)
4-17814898-G-A		not specified	Uncertain significance (Nov 15, 2021)
4-17814949-T-C		not specified	Uncertain significance (Sep 17, 2021)
4-17815326-T-C		not specified	Uncertain significance (Jul 26, 2022)
4-17817327-T-C		not specified	Uncertain significance (Oct 18, 2021)
4-17817337-G-C		not specified	Uncertain significance (Jun 11, 2021)
4-17817404-A-G		not specified	Likely benign (Feb 21, 2024)
4-17817961-T-G		not specified	Uncertain significance (Mar 08, 2024)
4-17817994-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-17818048-A-G		not specified	Uncertain significance (Jun 24, 2022)
4-17823002-G-C		not specified	Uncertain significance (Dec 13, 2023)
4-17823649-A-T		not specified	Uncertain significance (Jun 22, 2023)
4-17824993-G-A		not specified	Uncertain significance (Mar 01, 2024)
4-17825019-A-G		not specified	Uncertain significance (Nov 10, 2022)
4-17825416-A-T		not specified	Uncertain significance (May 15, 2023)
4-17825485-A-C		not specified	Uncertain significance (Nov 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAPG	protein_coding	protein_coding	ENST00000251496	21	33961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.08e-7	1.00	125676	0	69	125745	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	427	496	0.861	0.0000238	6635
Missense in Polyphen		69	92.714	0.74422		1238
Synonymous	1.56	155	182	0.853	0.00000910	1922
Loss of Function	3.69	19	46.0	0.413	0.00000211	669

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000178
Ashkenazi Jewish	0.000208	0.000198
East Asian	0.000342	0.000326
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000267	0.000255
Middle Eastern	0.000342	0.000326
South Asian	0.000787	0.000653
Other	0.00104	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit 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 Prometaphase Chromosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.0928

Intolerance Scores

• loftool: 0.775
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.83

Haploinsufficiency Scores

• pHI: 0.249
• hipred: Y
• hipred_score: 0.756
• ghis: 0.717

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncapg

Zebrafish Information Network

• Gene name: ncapg
• Affected structure: gastrula cell
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: mitotic chromosome condensation;cell division
• Cellular component: condensed chromosome, centromeric region;condensed chromosome;condensin complex;nucleus;cytoplasm;cytosol;membrane
• Molecular function: protein binding