DCDC2B

doublecortin domain containing 2B, the group of Doublecortin superfamily

Basic information

Region (hg38): 1:32209089-32216192

Links

ENSG00000222046 ∙ NCBI:149069 ∙ ∙ HGNC:32576 ∙ Uniprot:A2VCK2 ∙ 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 DCDC2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCDC2B 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						0
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in DCDC2B

This is a list of pathogenic ClinVar variants found in the DCDC2B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32209137-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-32209142-G-A		not specified	Uncertain significance (Nov 13, 2024)
1-32209182-A-G		not specified	Uncertain significance (Apr 12, 2024)
1-32209184-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-32209187-C-T		not specified	Uncertain significance (Oct 09, 2024)
1-32209200-T-C		not specified	Uncertain significance (Nov 13, 2024)
1-32209217-G-A		not specified	Uncertain significance (Jul 15, 2021)
1-32209219-G-C		not specified	Uncertain significance (Apr 25, 2023)
1-32209232-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-32209253-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-32209257-C-T		not specified	Uncertain significance (Jul 27, 2024)
1-32209298-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-32209299-C-A		not specified	Uncertain significance (Feb 15, 2023)
1-32209302-A-G		not specified	Uncertain significance (Nov 08, 2021)
1-32209314-G-T		not specified	Uncertain significance (Nov 26, 2024)
1-32211798-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-32211815-G-C		not specified	Uncertain significance (Aug 02, 2021)
1-32211819-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-32212084-G-C		not specified	Uncertain significance (Mar 19, 2024)
1-32212086-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-32212092-G-A		not specified	Uncertain significance (May 28, 2024)
1-32212105-T-G		not specified	Uncertain significance (Jul 21, 2022)
1-32212149-G-T		not specified	Uncertain significance (Oct 17, 2023)
1-32212159-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-32212186-G-A		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCDC2B	protein_coding	protein_coding	ENST00000409358	9	7103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.04e-8	0.443	121923	23	2720	124666	0.0111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.194	201	193	1.04	0.00000984	2209
Missense in Polyphen		45	55.338	0.81318		642
Synonymous	-0.997	89	77.8	1.14	0.00000385	743
Loss of Function	0.896	14	18.1	0.773	0.00000104	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00742	0.00742
Ashkenazi Jewish	0.00567	0.00558
East Asian	0.000278	0.000278
Finnish	0.0143	0.0142
European (Non-Finnish)	0.0181	0.0181
Middle Eastern	0.000278	0.000278
South Asian	0.00324	0.00324
Other	0.0106	0.0106

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcdc2b

Zebrafish Information Network

• Gene name: dcdc2b
• Affected structure: neuromast hair cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: intracellular signal transduction
• Cellular component: microtubule organizing center;microtubule;cortical actin cytoskeleton
• Molecular function: protein binding