CD44

CD44 molecule (Indian blood group), the group of CD molecules|Proteoglycans|Blood group antigens

Basic information

Region (hg38): 11:35138882-35232402

Previous symbols: [ "MIC4", "MDU2", "MDU3" ]

Links

ENSG00000026508 ∙ NCBI:960 ∙ OMIM:107269 ∙ HGNC:1681 ∙ Uniprot:P16070 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Indian	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	1146277; 8636151

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD44 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD44 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				6	7	13
missense			30	3	5	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1	3		4
Total	0	0	31	12	12

Variants in CD44

This is a list of pathogenic ClinVar variants found in the CD44 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-35139361-G-A		not specified	Uncertain significance (Aug 04, 2023)
11-35150575-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35153498-T-C		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35158104-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35163005-A-T		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35166644-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35169898-C-G		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35170667-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35170732-A-G		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35171082-C-T		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35176617-A-C		not specified	Uncertain significance (Jan 24, 2023)
11-35176643-C-T		not specified	Uncertain significance (Mar 17, 2023)
11-35176644-G-A		INDIAN BLOOD GROUP SYSTEM POLYMORPHISM	Benign (Jan 15, 1994)
11-35176654-C-T			Likely benign (May 25, 2018)
11-35176696-G-T		not specified	Uncertain significance (May 08, 2024)
11-35179369-G-A		Calcium oxalate urolithiasis	association (Mar 01, 2014)
11-35180295-C-T		CD44-related disorder	Benign (Oct 21, 2019)
11-35180309-G-A		not specified	Uncertain significance (May 12, 2024)
11-35180369-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-35180385-C-T			Likely benign (May 24, 2018)
11-35180414-T-C			Benign (Jul 23, 2018)
11-35189836-T-G			Likely benign (Jul 21, 2018)
11-35189886-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-35189887-G-A		CD44-related disorder	Benign (Jul 23, 2018)
11-35189914-C-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD44	protein_coding	protein_coding	ENST00000428726	18	93533

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.45e-7	1.00	125637	0	110	125747	0.000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.842	358	406	0.882	0.0000206	4882
Missense in Polyphen		84	116.28	0.72241		1369
Synonymous	-0.0275	145	145	1.00	0.00000775	1399
Loss of Function	3.25	18	40.2	0.448	0.00000206	461

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00122	0.00122
Ashkenazi Jewish	0.00	0.00
East Asian	0.00229	0.00229
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.00229	0.00229
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for hyaluronic acid (HA). Mediates cell-cell and cell-matrix interactions through its affinity for HA, and possibly also through its affinity for other ligands such as osteopontin, collagens, and matrix metalloproteinases (MMPs). Adhesion with HA plays an important role in cell migration, tumor growth and progression. In cancer cells, may play an important role in invadopodia formation. Also involved in lymphocyte activation, recirculation and homing, and in hematopoiesis. Altered expression or dysfunction causes numerous pathogenic phenotypes. Great protein heterogeneity due to numerous alternative splicing and post-translational modification events. Receptor for LGALS9; the interaction enhances binding of SMAD3 to the FOXP3 promoter, leading to up-regulation of FOXP3 expression and increased induced regulatory T (iTreg) cell stability and suppressive function (By similarity). {ECO:0000250|UniProtKB:P15379, ECO:0000269|PubMed:16541107}.
• Pathway: ECM-receptor interaction - Homo sapiens (human);Shigellosis - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Hepatitis C and Hepatocellular Carcinoma;Wnt Signaling Pathway and Pluripotency;Senescence and Autophagy in Cancer;Neutrophil degranulation;Hyaluronan uptake and degradation;Hyaluronan metabolism;Metabolism of carbohydrates;Cytokine Signaling in Immune system;Integrin cell surface interactions;Glycosaminoglycan metabolism;Extracellular matrix organization;Innate Immune System;Immune System;Metabolism;Integrin;TGF_beta_Receptor;Cell surface interactions at the vascular wall;Hemostasis;Degradation of the extracellular matrix;Interferon gamma signaling;Wnt Canonical;Osteopontin-mediated events;Interferon Signaling;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.949

Intolerance Scores

• loftool: 0.890
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.52

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.598
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd44
• Phenotype: pigmentation phenotype; neoplasm; 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); hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; muscle phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); endocrine/exocrine gland 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: inflammatory response;cell adhesion;cell-matrix adhesion;extracellular matrix disassembly;extracellular matrix organization;hyaluronan catabolic process;positive regulation of peptidyl-serine phosphorylation;positive regulation of heterotypic cell-cell adhesion;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;neutrophil degranulation;negative regulation of DNA damage response, signal transduction by p53 class mediator;wound healing, spreading of cells;cellular response to fibroblast growth factor stimulus;positive regulation of peptidyl-tyrosine phosphorylation;leukocyte migration;cartilage development;interferon-gamma-mediated signaling pathway;positive regulation of ERK1 and ERK2 cascade;monocyte aggregation;cell-cell adhesion;positive regulation of monocyte aggregation;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;regulation of lamellipodium morphogenesis
• Cellular component: Golgi apparatus;cytosol;plasma membrane;integral component of plasma membrane;microvillus;focal adhesion;cell surface;basolateral plasma membrane;apical plasma membrane;secretory granule membrane;lamellipodium membrane;macrophage migration inhibitory factor receptor complex;cell projection;extracellular exosome
• Molecular function: transmembrane signaling receptor activity;cytokine receptor activity;protein binding;collagen binding;hyaluronic acid binding