NCDN

neurochondrin, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 1:35557473-35567274

Links

ENSG00000020129 ∙ NCBI:23154 ∙ OMIM:608458 ∙ HGNC:17597 ∙ Uniprot:Q9UBB6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• neurodevelopmental disorder with infantile epileptic spasms (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with infantile epileptic spasms	AD	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	Craniofacial; Musculoskeletal; Neurologic	33711248

ClinVar

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

• not_specified (71 variants)
• not_provided (28 variants)
• Neurodevelopmental_disorder_with_infantile_epileptic_spasms (23 variants)
• NCDN-related_disorder (6 variants)
• Floating-Harbor_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCDN gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014284.3. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				14	1	15
missense	3	2	88	6		99
nonsense			1			1
start loss						0
frameshift		2				2
splice donor/acceptor (+/-2bp)			4			4
Total	3	4	93	20	1

Highest pathogenic variant AF is 6.84369e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NCDN	protein_coding	protein_coding	ENST00000373243	7	9802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125715	0	5	125720	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.76	235	463	0.508	0.0000303	4608
Missense in Polyphen		35	121.62	0.28779		1273
Synonymous	0.732	203	217	0.937	0.0000148	1647
Loss of Function	4.65	1	27.1	0.0369	0.00000134	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in signal transduction, in the nervous system, via increasing cell surface localization of GRM5 and positively regulating its signaling (By similarity). Required for the spatial learning process. Acts as a negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in modulating melanin- concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:16945926}.
• Pathway: Splicing factor NOVA regulated synaptic proteins (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.0479
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Gene ontology

• Biological process: neuron projection development;bone resorption;regulation of neuronal synaptic plasticity
• Cellular component: nucleus;cytosol;membrane;axon;dendrite;neuronal cell body
• Molecular function: protein binding