DIP2C

disco interacting protein 2 homolog C, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 10:274201-689668

Previous symbols: [ "KIAA0934" ]

Links

ENSG00000151240

∙ NCBI:22982 ∙ OMIM:611380 ∙ HGNC:29150 ∙ Uniprot:Q9Y2E4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

complex neurodevelopmental disorder (Definitive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DIP2C gene.

not_provided (809 variants)
Inborn_genetic_diseases (147 variants)
DIP2C-related_disorder (31 variants)
Neurodevelopmental_disorder (4 variants)
See_cases (2 variants)
Obesity (1 variants)
Streaky_metaphyseal_sclerosis (1 variants)
DIP2C-associated_disorder (1 variants)
not_specified (1 variants)
Neurodevelopmental_delay (1 variants)
Aplasia/Hypoplasia_of_the_phalanges_of_the_4th_toe (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIP2C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014974.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	269 clinvar	33 clinvar	308
missense			317 clinvar	19 clinvar	2 clinvar	338
nonsense	4 clinvar	1 clinvar	2 clinvar			7
start loss						0
frameshift	7 clinvar	1 clinvar	8 clinvar			16
splice donor/acceptor (+/-2bp)		1 clinvar	3 clinvar			4
Total	11	3	336	288	35

Highest pathogenic variant AF is 0.00000205271

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DIP2C	protein_coding	protein_coding	ENST00000280886	37	415554

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.92e-10	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.67	584	999	0.584	0.0000654	10025
Missense in Polyphen		198	449.09	0.44089		4327
Synonymous	-3.36	524	435	1.21	0.0000331	3211
Loss of Function	8.01	7	88.1	0.0794	0.00000478	936

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000398	0.000398
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

loftool: 0.356
rvis_EVS: -3.62
rvis_percentile_EVS: 0.29

Haploinsufficiency Scores

pHI: 0.198
hipred: Y
hipred_score: 0.563
ghis: 0.613

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.750

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dip2c
Phenotype

Gene ontology

Biological process: biological_process
Cellular component: cellular_component
Molecular function: molecular_function;catalytic activity