NCAPH2

non-SMC condensin II complex subunit H2, the group of Condensin II subunits

Basic information

Region (hg38): 22:50508223-50524780

Links

ENSG00000025770 ∙ NCBI:29781 ∙ OMIM:611230 ∙ HGNC:25071 ∙ Uniprot:Q6IBW4 ∙ 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 NCAPH2 gene.

• not provided (21 variants)
• Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 1 (5 variants)
• Myopia 6 (2 variants)
• Seizure;Severe global developmental delay (1 variants)
• Tip-toe gait (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAPH2 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					2	2
missense			41	3	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding	22	20	150	140	5	337
Total	22	20	191	143	8

Highest pathogenic variant AF is 0.000105

Variants in NCAPH2

This is a list of pathogenic ClinVar variants found in the NCAPH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50516456-A-G		not specified	Uncertain significance (May 24, 2024)
22-50516499-T-C		not specified	Uncertain significance (Nov 12, 2021)
22-50517635-G-A		not specified	Likely benign (Oct 12, 2022)
22-50517642-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-50517802-C-T		not specified	Uncertain significance (Dec 15, 2023)
22-50517805-C-T		not specified	Uncertain significance (Sep 27, 2021)
22-50517991-C-T		not specified	Uncertain significance (Feb 22, 2023)
22-50518031-A-G		not specified	Uncertain significance (Aug 30, 2021)
22-50518180-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-50518194-C-G		not specified	Uncertain significance (Sep 16, 2021)
22-50518218-C-T		not specified	Uncertain significance (Jan 20, 2023)
22-50518248-G-C		not specified	Uncertain significance (Aug 19, 2023)
22-50518654-G-A		not specified	Likely benign (Aug 21, 2023)
22-50518675-A-G		not specified	Uncertain significance (Sep 06, 2022)
22-50518686-C-T			Benign (Mar 29, 2018)
22-50518687-G-A		not specified	Uncertain significance (Oct 26, 2022)
22-50518703-T-C		not specified	Uncertain significance (Mar 25, 2024)
22-50518731-A-G			Likely benign (Aug 01, 2022)
22-50519196-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-50519210-A-C		not specified	Uncertain significance (Dec 14, 2023)
22-50519225-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-50519285-G-A		not specified	Likely benign (Feb 12, 2024)
22-50520996-G-A		not specified	Uncertain significance (Aug 12, 2022)
22-50521007-G-C		not specified	Uncertain significance (Nov 15, 2021)
22-50521022-G-A		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAPH2	protein_coding	protein_coding	ENST00000299821	20	15257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000288	1.00	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.176	346	355	0.974	0.0000214	3945
Missense in Polyphen		101	124.3	0.81255		1510
Synonymous	-2.66	189	148	1.28	0.00000964	1159
Loss of Function	3.66	13	37.1	0.351	0.00000175	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.000243	0.000231
European (Non-Finnish)	0.000181	0.000167
Middle Eastern	0.000111	0.000109
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of the condensin-2 complex, a complex that seems to provide chromosomes with an additional level of organization and rigidity and in establishing mitotic chromosome architecture. May play a role in lineage-specific role in T-cell development (By similarity). {ECO:0000250, ECO:0000269|PubMed:14532007}.
• Pathway: Condensation of Prophase Chromosomes;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.0969

Intolerance Scores

• loftool: 0.0236
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.66

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.456
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.631

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncaph2
• Phenotype: immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); hematopoietic system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: meiotic chromosome condensation;T cell differentiation in thymus;chromosome organization;mitotic sister chromatid separation;female meiosis chromosome separation
• Cellular component: condensed chromosome;condensin complex;nucleus;nucleoplasm;membrane;cell junction;intercellular bridge
• Molecular function: chromatin binding;protein binding