DCDC1

doublecortin domain containing 1, the group of Doublecortin superfamily

Basic information

Region (hg38): 11:30830368-31369810

Previous symbols: [ "DCDC5" ]

Links

ENSG00000170959 ∙ NCBI:341019 ∙ OMIM:608062 ∙ HGNC:20625 ∙ Uniprot:M0R2J8 ∙ 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 DCDC1 gene.

• not provided (21 variants)
• Inborn genetic diseases (11 variants)
• Head and neck cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCDC1 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				2	3	5
missense			14	1	7	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	3	5
Total	0	0	14	5	13

Variants in DCDC1

This is a list of pathogenic ClinVar variants found in the DCDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-30881290-A-G			Benign (May 08, 2018)
11-30894328-G-T			Uncertain significance (Mar 01, 2024)
11-30899570-G-A		not specified	Uncertain significance (Jul 14, 2021)
11-30899605-C-G			Benign (Dec 31, 2019)
11-30899619-C-T			Benign (Oct 01, 2023)
11-30903511-T-C			Benign (May 08, 2018)
11-30903545-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-30903613-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-30904978-C-T			Benign (May 08, 2018)
11-30905154-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-30906554-T-C			Likely benign (Jul 01, 2022)
11-30906655-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-30916912-T-C		not specified	Uncertain significance (Jul 13, 2021)
11-30920891-G-A		DCDC1-related disorder	Benign (Jun 04, 2019)
11-30925360-A-T		not specified	Uncertain significance (Oct 26, 2021)
11-30925373-C-T		not specified	Uncertain significance (Aug 04, 2021)
11-30931781-G-A		not specified	Likely benign (Jul 09, 2021)
11-30931871-A-G		not specified	Uncertain significance (Oct 18, 2021)
11-30952507-T-C		DCDC1-related disorder	Likely benign (Sep 30, 2019)
11-30952568-C-A		DCDC1-related disorder	Benign (Jun 25, 2019)
11-31064568-G-T		DCDC1-related disorder	Benign (Feb 07, 2020)
11-31065144-G-C		DCDC1-related disorder	Benign (Jan 13, 2020)
11-31077857-G-A		DCDC1-related disorder	Benign (May 14, 2019)
11-31077909-A-C		DCDC1-related disorder	Benign (Nov 25, 2019)
11-31091437-A-G		DCDC1-related disorder	Likely benign (Jul 15, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCDC1	protein_coding	protein_coding	ENST00000452803	7	539442

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.79e-8	0.393	125651	0	15	125666	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0429	178	176	1.01	0.00000841	2297
Missense in Polyphen		40	42.434	0.94264		562
Synonymous	-0.602	72	65.8	1.09	0.00000332	672
Loss of Function	0.758	13	16.3	0.798	8.70e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000350
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.0000560	0.0000528
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0343

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.0233
• hipred: N
• hipred_score: 0.123
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcdc5

Gene ontology

• Biological process: intracellular signal transduction