CD74

CD74 molecule, the group of CD molecules

Basic information

Region (hg38): 5:150401636-150412969

Previous symbols: [ "DHLAG" ]

Links

ENSG00000019582 ∙ NCBI:972 ∙ OMIM:142790 ∙ HGNC:1697 ∙ Uniprot:P04233 ∙ 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 CD74 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD74 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			6			6
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	6	0	0

Variants in CD74

This is a list of pathogenic ClinVar variants found in the CD74 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-150402253-G-A			Likely benign (Jul 01, 2022)
5-150402602-A-G		not specified	Uncertain significance (Jul 29, 2022)
5-150403307-T-G		not specified	Uncertain significance (Aug 03, 2022)
5-150404685-G-A		not specified	Uncertain significance (Dec 06, 2022)
5-150407263-C-T		not specified	Uncertain significance (Jun 13, 2023)
5-150407313-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-150412631-G-A		not specified	Uncertain significance (Jan 17, 2024)
5-150412647-G-C		not specified	Uncertain significance (Oct 06, 2021)
5-150412724-C-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD74	protein_coding	protein_coding	ENST00000009530	9	11293

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.249	0.750	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	125	177	0.704	0.0000103	1932
Missense in Polyphen		41	67.553	0.60693		706
Synonymous	0.457	67	71.9	0.931	0.00000451	552
Loss of Function	2.81	4	16.2	0.246	7.89e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF.
• Disease: DISEASE: Note=A chromosomal aberration involving CD74 is found in a non-small cell lung tumor. Results in the formation of a CD74- ROS1 chimeric protein. {ECO:0000269|PubMed:12661006}.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Macrophage markers;Macrophage markers;antigen processing and presentation;MHC class II antigen presentation;Immune System;Adaptive Immune System;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.354

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.311
• hipred: Y
• hipred_score: 0.508
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Mouse Genome Informatics

• Gene name: Cd74
• Phenotype: immune system phenotype; skeleton 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); hematopoietic system phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: activation of MAPK activity;prostaglandin biosynthetic process;positive regulation of protein phosphorylation;positive regulation of cytokine-mediated signaling pathway;positive regulation of dendritic cell antigen processing and presentation;negative regulation of peptide secretion;positive regulation of type 2 immune response;negative regulation of mature B cell apoptotic process;intracellular protein transport;defense response;signal transduction;cell population proliferation;immunoglobulin mediated immune response;antigen processing and presentation of endogenous antigen;antigen processing and presentation of exogenous peptide antigen via MHC class II;positive regulation of B cell proliferation;positive regulation of kinase activity;macrophage migration inhibitory factor signaling pathway;regulation of macrophage activation;negative regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of MAPK cascade;negative regulation of DNA damage response, signal transduction by p53 class mediator;T cell selection;positive thymic T cell selection;negative thymic T cell selection;negative regulation of T cell differentiation;positive regulation of T cell differentiation;positive regulation of monocyte differentiation;positive regulation of transcription, DNA-templated;positive regulation of viral entry into host cell;positive regulation of fibroblast proliferation;positive regulation of peptidyl-tyrosine phosphorylation;leukocyte migration;chaperone cofactor-dependent protein refolding;protein heterotetramerization;positive regulation of macrophage cytokine production;protein-containing complex assembly;protein trimerization;positive regulation of ERK1 and ERK2 cascade;positive regulation of neutrophil chemotaxis;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of chemokine (C-X-C motif) ligand 2 production
• Cellular component: Golgi membrane;lysosomal membrane;multivesicular body;vacuole;plasma membrane;external side of plasma membrane;cell surface;ER to Golgi transport vesicle membrane;membrane;integral component of membrane;transport vesicle membrane;endocytic vesicle membrane;clathrin-coated endocytic vesicle membrane;trans-Golgi network membrane;macrophage migration inhibitory factor receptor complex;NOS2-CD74 complex;MHC class II protein complex;lysosomal lumen;extracellular exosome;integral component of lumenal side of endoplasmic reticulum membrane
• Molecular function: amyloid-beta binding;cytokine receptor activity;protein binding;cytokine binding;MHC class II protein complex binding;macrophage migration inhibitory factor binding;MHC class II protein binding;CD4 receptor binding;MHC class II protein binding, via antigen binding groove;identical protein binding;protein folding chaperone;nitric-oxide synthase binding