NCAPG2

non-SMC condensin II complex subunit G2, the group of Armadillo like helical domain containing|Condensin II subunits

Basic information

Region (hg38): 7:158631169-158704804

Previous symbols: [ "LUZP5" ]

Links

ENSG00000146918 ∙ NCBI:54892 ∙ OMIM:608532 ∙ HGNC:21904 ∙ Uniprot:Q86XI2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Khan-Khan-Katsanis syndrome (Limited), mode of inheritance: AR
• Khan-Khan-Katsanis syndrome (Limited), mode of inheritance: AR
• Khan-Khan-Katsanis syndrome (Limited), mode of inheritance: Unknown
• Khan-Khan-Katsanis syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Kahn-Kahn-Katsanis syndrome	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal	30609410

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NCAPG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAPG2 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				6	3	9
missense			77	10	3	90
nonsense		1				1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	2	1	4
non coding					2	2
Total	0	1	79	16	8

Variants in NCAPG2

This is a list of pathogenic ClinVar variants found in the NCAPG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-158631709-T-C		not specified	Uncertain significance (Jul 14, 2023)
7-158641559-GAAAAAAA-G		NCAPG2-related disorder	Benign (Nov 06, 2019)
7-158644317-T-C		not specified	Uncertain significance (Apr 04, 2024)
7-158644322-A-G		not specified	Uncertain significance (Jan 02, 2025)
7-158644368-CT-C			Uncertain significance (-)
7-158645564-C-T		not specified	Uncertain significance (Jun 07, 2024)
7-158646467-C-T		not specified	Uncertain significance (Mar 24, 2023)
7-158646471-C-T		NCAPG2-related disorder	Likely benign (Sep 01, 2024)
7-158646502-C-T		not specified	Uncertain significance (Dec 23, 2024)
7-158646554-C-T		not specified	Conflicting classifications of pathogenicity (Oct 18, 2021)
7-158650885-G-C		not specified	Uncertain significance (Nov 21, 2023)
7-158650891-C-G		not specified	Uncertain significance (Feb 28, 2024)
7-158650891-C-T		not specified	Uncertain significance (Nov 12, 2024)
7-158650893-C-T		not specified	Uncertain significance (May 09, 2024)
7-158650901-A-C			Likely benign (Mar 01, 2025)
7-158650918-G-A			Likely benign (Mar 01, 2024)
7-158652283-T-G		Khan-Khan-Katsanis syndrome	Benign (Sep 05, 2021)
7-158652307-C-T		not specified	Uncertain significance (Jul 27, 2024)
7-158652327-C-T		not specified	Uncertain significance (Jul 14, 2022)
7-158652329-T-G			Likely benign (Jan 01, 2023)
7-158652371-G-C		NCAPG2-related disorder	Benign (Sep 19, 2018)
7-158652412-G-C		Khan-Khan-Katsanis syndrome	Uncertain significance (May 23, 2022)
7-158654618-C-T		not specified	Uncertain significance (Nov 21, 2023)
7-158654630-T-C		not specified	Uncertain significance (Jan 01, 2025)
7-158654645-T-C		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAPG2	protein_coding	protein_coding	ENST00000409423	27	73518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.978	0.0224	124778	0	35	124813	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	484	620	0.781	0.0000334	7510
Missense in Polyphen		122	188.97	0.6456		2329
Synonymous	1.17	206	229	0.901	0.0000129	2128
Loss of Function	5.87	11	60.2	0.183	0.00000287	775

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000415
Ashkenazi Jewish	0.000324	0.000298
East Asian	0.000168	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000168	0.000167
South Asian	0.000236	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of the condensin-2 complex, a complex which establishes mitotic chromosome architecture and is involved in physical rigidity of the chromatid axis. {ECO:0000269|PubMed:14532007}.
• Pathway: Mesodermal Commitment Pathway;Condensation of Prophase Chromosomes;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• loftool: 0.619
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.65

Haploinsufficiency Scores

• pHI: 0.734
• hipred: Y
• hipred_score: 0.708
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncapg2
• Phenotype: embryo phenotype; 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: inner cell mass cell proliferation;transcription by RNA polymerase II;cell cycle;erythrocyte differentiation;chromosome condensation;negative regulation of erythrocyte differentiation;cell division;positive regulation of protein tyrosine kinase activity;positive regulation of signaling receptor activity
• Cellular component: condensin complex;nucleoplasm;membrane;nuclear speck
• Molecular function: methylated histone binding;bHLH transcription factor binding;molecular function regulator