DIP2A

disco interacting protein 2 homolog A

Basic information

Region (hg38): 21:46458890-46570015

Previous symbols: [ "C21orf106" ]

Links

ENSG00000160305 ∙ NCBI:23181 ∙ OMIM:607711 ∙ HGNC:17217 ∙ Uniprot:Q14689 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DIP2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIP2A 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			1	6	10	17
missense			92	10	1	103
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1	1			2
splice region			1	2	2	5
non coding				1		1
Total	0	1	95	17	11

Variants in DIP2A

This is a list of pathogenic ClinVar variants found in the DIP2A region.

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

Position	Type	Phenotype	Significance	ClinVar
21-46459158-G-C		not specified	Uncertain significance (Mar 07, 2024)
21-46459230-G-A		DIP2A-related disorder	Likely benign (Aug 21, 2019)
21-46484774-G-A			Uncertain significance (Jul 01, 2023)
21-46484793-C-G		not specified	Uncertain significance (Dec 15, 2022)
21-46490610-A-G		DIP2A-related disorder	Benign (May 15, 2020)
21-46490625-G-T		DIP2A-related disorder	Uncertain significance (Dec 17, 2023)
21-46490629-A-G		not specified	Uncertain significance (Nov 07, 2022)
21-46490692-G-A		not specified	Likely benign (Mar 29, 2023)
21-46490714-G-T		not specified	Uncertain significance (Sep 07, 2022)
21-46497075-T-C		not specified	Uncertain significance (Oct 03, 2022)
21-46497081-C-T		not specified	Uncertain significance (Jun 21, 2023)
21-46497082-G-A		DIP2A-related disorder	Likely benign (Jan 01, 2023)
21-46498618-G-A		not specified	Uncertain significance (Jul 20, 2021)
21-46498621-G-A		not specified	Uncertain significance (Jul 30, 2023)
21-46498636-C-T		not specified	Uncertain significance (Nov 22, 2023)
21-46498645-C-T		not specified	Uncertain significance (Jun 01, 2023)
21-46498694-G-C		not specified	Uncertain significance (Apr 18, 2023)
21-46498735-A-C		not specified	Uncertain significance (Apr 20, 2024)
21-46498801-C-T		not specified	Uncertain significance (Aug 12, 2022)
21-46504399-G-A		not specified	Uncertain significance (Feb 17, 2023)
21-46504406-A-G		not specified	Uncertain significance (Feb 22, 2023)
21-46504409-C-T		not specified	Uncertain significance (Oct 05, 2023)
21-46509259-G-A		not specified	Uncertain significance (Jan 29, 2024)
21-46509322-A-C		Autism spectrum disorder	Likely benign (Aug 16, 2021)
21-46509326-G-A		not specified	Uncertain significance (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DIP2A	protein_coding	protein_coding	ENST00000417564	38	111115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.113	0.887	125695	0	34	125729	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	729	957	0.761	0.0000612	9957
Missense in Polyphen		336	474.28	0.70844		4928
Synonymous	0.496	415	428	0.970	0.0000314	3368
Loss of Function	6.13	18	75.4	0.239	0.00000355	909

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000112	0.000109
South Asian	0.000166	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May provide positional cues for axon pathfinding and patterning in the central nervous system.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• loftool: 0.457
• rvis_EVS: -2.78
• rvis_percentile_EVS: 0.68

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.575
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.864

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dip2a

Gene ontology

• Biological process: multicellular organism development;negative regulation of gene expression;regulation of apoptotic process
• Cellular component: nucleus;cell surface
• Molecular function: catalytic activity;protein binding