DIP2C

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

Basic information

Region (hg38): 10:274189-689668

Previous symbols: [ "KIAA0934" ]

Links

ENSG00000151240 ∙ NCBI:22982 ∙ OMIM:611380 ∙ HGNC:29150 ∙ Uniprot:Q9Y2E4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not provided (479 variants)
• Inborn genetic diseases (38 variants)
• Neurodevelopmental disorder (4 variants)
• DIP2C-related condition (3 variants)
• Global developmental delay (1 variants)
• Obesity;Neurodevelopmental delay (1 variants)
• Streaky metaphyseal sclerosis;Aplasia/Hypoplasia of the phalanges of the 4th toe (1 variants)
• See cases (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.

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			4	163	37	204
missense			141	4	2	147
nonsense			3			3
start loss						0
frameshift			5			5
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region			8	28	6	42
non coding			2	88	21	111
Total	0	0	157	255	60

Variants in DIP2C

This is a list of pathogenic ClinVar variants found in the DIP2C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-277331-G-A			Likely benign (Oct 04, 2023)
10-277337-G-C			Likely benign (May 23, 2023)
10-277343-A-G		DIP2C-related disorder	Benign (Jan 31, 2024)
10-277364-T-C			Likely benign (Jul 12, 2022)
10-277376-G-A			Likely benign (May 15, 2023)
10-277381-G-A			Uncertain significance (Aug 01, 2019)
10-277403-C-A			Likely benign (Jun 15, 2022)
10-277423-T-C		Inborn genetic diseases	Uncertain significance (Feb 13, 2024)
10-277426-C-T			Uncertain significance (Jul 25, 2023)
10-277427-G-A		DIP2C-related disorder	Benign (Jan 22, 2024)
10-277429-C-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
10-277430-G-A			Likely benign (Feb 15, 2023)
10-277431-A-C			Uncertain significance (Jan 28, 2024)
10-277442-G-A			Likely benign (Sep 07, 2021)
10-277454-G-A			Likely benign (Jan 18, 2024)
10-277457-G-A			Likely benign (Nov 04, 2021)
10-277457-G-T			Likely benign (Oct 07, 2022)
10-277493-C-T			Likely benign (Nov 27, 2023)
10-277502-C-T			Benign (Jan 24, 2024)
10-277520-T-G			Uncertain significance (Sep 01, 2021)
10-277523-C-T			Likely benign (Dec 30, 2022)
10-277539-A-G			Uncertain significance (Jun 14, 2022)
10-277559-T-G			Benign (Jan 22, 2024)
10-277571-C-G			Likely benign (Nov 10, 2021)
10-277581-A-G			Likely benign (Oct 28, 2022)

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

Gene ontology

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