DDR1

discoidin domain receptor tyrosine kinase 1, the group of MicroRNA protein coding host genes|CD molecules|Receptor tyrosine kinases

Basic information

Region (hg38): 6:30876420-30900156

Previous symbols: [ "NTRK4", "PTK3A", "NEP", "CAK", "EDDR1" ]

Links

ENSG00000204580 ∙ NCBI:780 ∙ OMIM:600408 ∙ HGNC:2730 ∙ Uniprot:Q08345 ∙ 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 DDR1 gene.

• Inborn genetic diseases (21 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDR1 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		1
missense			19	4		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	5	0

Variants in DDR1

This is a list of pathogenic ClinVar variants found in the DDR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-30888778-A-G			Likely benign (Jun 05, 2018)
6-30889004-A-G		not specified	Uncertain significance (Feb 21, 2024)
6-30889209-A-G		not specified	Uncertain significance (Jul 26, 2021)
6-30889417-G-A		not specified	Uncertain significance (Nov 04, 2023)
6-30891069-C-T		not specified	Uncertain significance (Feb 03, 2022)
6-30891383-G-A		not specified	Uncertain significance (Nov 30, 2022)
6-30891406-G-C		not specified	Uncertain significance (Mar 04, 2024)
6-30891422-A-G		not specified	Uncertain significance (Jan 30, 2024)
6-30892127-C-T		not specified	Uncertain significance (Feb 12, 2024)
6-30892329-C-T		not specified	Uncertain significance (Sep 20, 2023)
6-30892488-C-T		not specified	Uncertain significance (Jan 13, 2023)
6-30892489-G-A		not specified	Uncertain significance (Nov 30, 2022)
6-30892501-C-T		not specified	Uncertain significance (May 24, 2023)
6-30892530-T-C		not specified	Uncertain significance (Dec 21, 2022)
6-30893110-C-T		not specified	Uncertain significance (Nov 08, 2021)
6-30893115-G-C		not specified	Uncertain significance (Oct 13, 2023)
6-30893407-G-A		not specified	Uncertain significance (Sep 27, 2022)
6-30893411-G-C		not specified	Uncertain significance (Jan 10, 2022)
6-30894606-C-T		not specified	Uncertain significance (Dec 06, 2023)
6-30894620-C-T			Likely benign (Aug 13, 2018)
6-30895461-C-T		not specified	Uncertain significance (Mar 20, 2023)
6-30895470-C-T		not specified	Uncertain significance (Sep 17, 2021)
6-30896638-A-G		not specified	Uncertain significance (Dec 20, 2023)
6-30896663-C-T		not specified	Uncertain significance (Mar 16, 2022)
6-30896706-C-T			Likely benign (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDR1	protein_coding	protein_coding	ENST00000376575	17	23736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000463	1.00	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	454	608	0.746	0.0000403	5910
Missense in Polyphen		109	163.49	0.66672		1586
Synonymous	1.85	208	245	0.850	0.0000157	1939
Loss of Function	3.74	17	43.7	0.389	0.00000225	451

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000180
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000356	0.000343
Middle Eastern	0.000109	0.000109
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell attachment to the extracellular matrix, remodeling of the extracellular matrix, cell migration, differentiation, survival and cell proliferation. Collagen binding triggers a signaling pathway that involves SRC and leads to the activation of MAP kinases. Regulates remodeling of the extracellular matrix by up-regulation of the matrix metalloproteinases MMP2, MMP7 and MMP9, and thereby facilitates cell migration and wound healing. Required for normal blastocyst implantation during pregnancy, for normal mammary gland differentiation and normal lactation. Required for normal ear morphology and normal hearing (By similarity). Promotes smooth muscle cell migration, and thereby contributes to arterial wound healing. Also plays a role in tumor cell invasion. Phosphorylates PTPN11. {ECO:0000250, ECO:0000269|PubMed:12065315, ECO:0000269|PubMed:16234985, ECO:0000269|PubMed:16337946, ECO:0000269|PubMed:19401332, ECO:0000269|PubMed:20093046, ECO:0000269|PubMed:20432435, ECO:0000269|PubMed:20884741, ECO:0000269|PubMed:21044884, ECO:0000269|PubMed:9659899}.
• Pathway: Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;Extracellular matrix organization;Non-integrin membrane-ECM interactions (Consensus)

Recessive Scores

• pRec: 0.343

Intolerance Scores

• loftool: 0.0429
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.31

Haploinsufficiency Scores

• pHI: 0.615
• hipred: Y
• hipred_score: 0.627
• ghis: 0.525

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddr1
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; hearing/vestibular/ear phenotype; craniofacial phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; skeleton phenotype

Gene ontology

• Biological process: regulation of cell growth;regulation of cell-matrix adhesion;cell adhesion;cell-matrix adhesion;transmembrane receptor protein tyrosine kinase signaling pathway;embryo implantation;lactation;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of extracellular matrix disassembly;smooth muscle cell migration;cell differentiation;extracellular matrix organization;collagen-activated tyrosine kinase receptor signaling pathway;peptidyl-tyrosine autophosphorylation;ear development;wound healing, spreading of cells;protein autophosphorylation;branching involved in mammary gland duct morphogenesis;mammary gland alveolus development;smooth muscle cell-matrix adhesion;axon development;regulation of extracellular matrix organization;neuron projection extension
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;receptor complex;extracellular exosome
• Molecular function: transmembrane receptor protein tyrosine kinase activity;protein binding;collagen binding;ATP binding;protein tyrosine kinase collagen receptor activity;metal ion binding