NCAPH

non-SMC condensin I complex subunit H, the group of Condensin I subunits|Kleisins

Basic information

Region (hg38): 2:96335766-96377091

Previous symbols: [ "BRRN1" ]

Links

ENSG00000121152

∙ NCBI:23397 ∙ OMIM:602332 ∙ HGNC:1112 ∙ Uniprot:Q15003 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

microcephaly 23, primary, autosomal recessive (Limited), mode of inheritance: Unknown
microcephaly 23, primary, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 23, primary, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	27737959

ClinVar

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

not_specified (98 variants)
not_provided (11 variants)
NCAPH-related_disorder (8 variants)
Microcephaly_23,_primary,_autosomal_recessive (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAPH gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015341.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense	1 clinvar		99 clinvar	6 clinvar	2 clinvar	108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	1	1	99	11	2

Highest pathogenic variant AF is 0.0000034581637

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAPH	protein_coding	protein_coding	ENST00000240423	18	38059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000801	1.00	125714	0	33	125747	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	353	416	0.849	0.0000223	4918
Missense in Polyphen		89	134.43	0.66208		1692
Synonymous	1.05	143	160	0.894	0.00000944	1383
Loss of Function	3.61	14	38.1	0.368	0.00000196	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000568	0.0000544
Finnish	0.000325	0.000323
European (Non-Finnish)	0.000133	0.000123
Middle Eastern	0.0000568	0.0000544
South Asian	0.000165	0.000163
Other	0.000490	0.000489

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: 0.123

Intolerance Scores

loftool: 0.655
rvis_EVS: -0.31
rvis_percentile_EVS: 32.17

Haploinsufficiency Scores

pHI: 0.640
hipred: Y
hipred_score: 0.765
ghis: 0.657

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: N
gene_indispensability_score: 0.264

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ncaph
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); 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); cellular phenotype;

Zebrafish Information Network

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

Gene ontology

Biological process: mitotic chromosome condensation;meiotic chromosome condensation;cell division;female meiosis chromosome separation;positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
Cellular component: condensin complex;nuclear condensin complex;nucleus;cytosol;membrane
Molecular function: chromatin binding;protein binding;DNA topoisomerase binding;DNA topoisomerase (ATP-hydrolyzing) activator activity