DIXDC1

DIX domain containing 1, the group of Dishevelled segment polarity proteins

Basic information

Region (hg38): 11:111927143-112022653

Links

ENSG00000150764 ∙ NCBI:85458 ∙ OMIM:610493 ∙ HGNC:23695 ∙ Uniprot:Q155Q3 ∙ 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 DIXDC1 gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIXDC1 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	2
missense			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	3

Variants in DIXDC1

This is a list of pathogenic ClinVar variants found in the DIXDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-111937554-A-G			Benign (Feb 25, 2018)
11-111964604-C-T		not specified	Uncertain significance (Oct 25, 2022)
11-111964612-C-G		not specified	Uncertain significance (Dec 05, 2022)
11-111964669-G-A		not specified	Uncertain significance (May 09, 2023)
11-111968615-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-111968626-A-G		not specified	Uncertain significance (Jan 02, 2024)
11-111974104-C-T		not specified	Uncertain significance (Aug 04, 2021)
11-111974119-G-A		not specified	Uncertain significance (Jun 05, 2023)
11-111974199-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-111974908-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-111980771-A-C		not specified	Uncertain significance (Dec 20, 2023)
11-111980774-G-A		not specified	Uncertain significance (Dec 31, 2023)
11-111982362-C-T		Obesity	Likely pathogenic (Dec 01, 2018)
11-111982371-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-111986900-T-C			Benign (Mar 29, 2018)
11-111993496-A-C		not specified	Uncertain significance (Mar 02, 2023)
11-111993710-G-T		not specified	Uncertain significance (Sep 27, 2021)
11-112016758-C-A		not specified	Uncertain significance (Dec 17, 2021)
11-112016758-C-T			Benign (Mar 29, 2018)
11-112019014-A-G		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DIXDC1	protein_coding	protein_coding	ENST00000440460	21	95441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.32e-11	0.998	137	124519	3	124659	0.967

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.41	292	368	0.793	0.0000203	4440
Missense in Polyphen		96	127.47	0.75311		1554
Synonymous	0.745	121	132	0.917	0.00000686	1241
Loss of Function	2.90	24	45.0	0.534	0.00000243	501

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.00	1.94
Ashkenazi Jewish	1.00	0.986
East Asian	1.00	0.976
Finnish	1.00	0.976
European (Non-Finnish)	1.00	0.963
Middle Eastern	1.00	0.976
South Asian	1.00	0.984
Other	1.00	0.955

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positive effector of the Wnt signaling pathway; activates WNT3A signaling via DVL2. Regulates JNK activation by AXIN1 and DVL2. {ECO:0000269|PubMed:15262978, ECO:0000269|PubMed:21189423}.

Recessive Scores

• pRec: 0.107

Haploinsufficiency Scores

• pHI: 0.286
• hipred: Y
• hipred_score: 0.637
• ghis: 0.528

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.118

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dixdc1
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; vision/eye phenotype

Gene ontology

• Biological process: cerebral cortex radially oriented cell migration;forebrain ventricular zone progenitor cell division;positive regulation of Wnt signaling pathway;regulation of actin cytoskeleton organization;negative regulation of neuron differentiation;canonical Wnt signaling pathway;regulation of microtubule cytoskeleton organization
• Cellular component: cytosol;cytoskeleton;focal adhesion
• Molecular function: actin binding;protein binding;protein domain specific binding;gamma-tubulin binding