NCAPD3

non-SMC condensin II complex subunit D3, the group of Condensin II subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 11:134150113-134225504

Links

ENSG00000151503 ∙ NCBI:23310 ∙ OMIM:609276 ∙ HGNC:28952 ∙ Uniprot:P42695 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive primary microcephaly (Supportive), mode of inheritance: AR
• microcephaly 22, primary, autosomal recessive (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 22, 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 NCAPD3 gene.

• Microcephaly 22, primary, autosomal recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCAPD3 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				24	5	29
missense			102	6	13	121
nonsense		2	1			3
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1	9		10
non coding			1		4	5
Total	1	3	105	30	22

Highest pathogenic variant AF is 0.0000329

Variants in NCAPD3

This is a list of pathogenic ClinVar variants found in the NCAPD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-134152936-G-A		NCAPD3-related disorder	Likely benign (Aug 20, 2024)
11-134152944-T-C		NCAPD3-related disorder	Likely benign (Sep 27, 2022)
11-134152958-T-A		not specified	Uncertain significance (May 04, 2022)
11-134152972-C-T		NCAPD3-related disorder	Benign (Dec 11, 2019)
11-134153006-T-C		not specified	Uncertain significance (Nov 07, 2022)
11-134153011-C-G		not specified	Uncertain significance (Dec 02, 2022)
11-134153015-C-T		not specified	Uncertain significance (Mar 30, 2022)
11-134153023-C-A		not specified	Uncertain significance (Jun 02, 2023)
11-134153139-C-T		Microcephaly 22, primary, autosomal recessive	Likely pathogenic (Mar 29, 2024)
11-134153173-T-C		not specified	Uncertain significance (Dec 14, 2023)
11-134153177-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-134153196-T-G		not specified	Uncertain significance (Jun 21, 2022)
11-134153281-G-T		NCAPD3-related disorder	Likely benign (Sep 13, 2023)
11-134153310-G-A		not specified	Uncertain significance (Jul 13, 2021)
11-134153322-T-C		not specified	Uncertain significance (Dec 12, 2023)
11-134153370-A-G		NCAPD3-related disorder	Likely benign (Sep 17, 2019)
11-134157022-G-C		NCAPD3-related disorder	Likely benign (Jun 06, 2019)
11-134157033-T-C		not specified	Uncertain significance (May 18, 2022)
11-134157048-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-134157049-G-T		NCAPD3-related disorder	Benign (Jan 01, 2024)
11-134157060-C-T		not specified	Uncertain significance (May 24, 2023)
11-134157939-G-A		Intellectual disability	Benign (Dec 31, 2019)
11-134157973-G-A		NCAPD3-related disorder	Uncertain significance (Mar 01, 2021)
11-134157990-C-T		NCAPD3-related disorder	Likely benign (Mar 21, 2022)
11-134157992-A-T		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCAPD3	protein_coding	protein_coding	ENST00000534548	35	75335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.82e-9	1.00	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.728	876	817	1.07	0.0000445	9807
Missense in Polyphen		136	178.05	0.76383		2239
Synonymous	-3.36	396	320	1.24	0.0000186	2863
Loss of Function	5.40	30	83.1	0.361	0.00000438	985

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000470	0.000470
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000384	0.000381
Finnish	0.000511	0.000508
European (Non-Finnish)	0.000363	0.000360
Middle Eastern	0.000384	0.000381
South Asian	0.000295	0.000294
Other	0.000816	0.000815

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: Condensation of Prophase Chromosomes;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.0997

Intolerance Scores

• loftool: 0.733
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.12

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.421
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.500

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ncapd3

Gene ontology

• Biological process: mitotic chromosome condensation;meiotic chromosome condensation;cell division;chromosome separation
• Cellular component: condensed chromosome, centromeric region;nuclear condensin complex;nucleoplasm;membrane;nuclear pericentric heterochromatin
• Molecular function: chromatin binding;protein binding;methylated histone binding;histone binding