CD320

CD320 molecule, the group of CD molecules

Basic information

Region (hg38): 19:8302127-8308358

Links

ENSG00000167775

∙ NCBI:51293 ∙ OMIM:606475 ∙ HGNC:16692 ∙ Uniprot:Q9NPF0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

methylmalonic acidemia due to transcobalamin receptor defect (Limited), mode of inheritance: AR
methylmalonic acidemia due to transcobalamin receptor defect (Limited), mode of inheritance: Unknown
methylmalonic acidemia due to transcobalamin receptor defect (Supportive), mode of inheritance: AR
methylmalonic acidemia due to transcobalamin receptor defect (Limited), mode of inheritance: Unknown
methylmalonic acidemia due to transcobalamin receptor defect (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Methylmalonic aciduria, transient, due to transcobalamin receptor defect	AR	Biochemical; Ophthalmologic	Medical treatment (eg, with IV B6 and IM B12-hydroxocobalamine) has been shown to positively affect laboratory parameters, and may be clinically beneficial though long-term clinical sequelae are unclear	Biochemical; Ophthalmologic	20524213; 22819238

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD320 gene.

Methylmalonic_acidemia_due_to_transcobalamin_receptor_defect (138 variants)
not_specified (51 variants)
not_provided (21 variants)
CD320-related_disorder (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD320 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016579.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	35 clinvar	3 clinvar	40
missense			95 clinvar	8 clinvar	2 clinvar	105
nonsense			2 clinvar			2
start loss			1			1
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	43	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD320	protein_coding	protein_coding	ENST00000301458	5	6230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00352	0.851	125668	0	19	125687	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.244	160	169	0.947	0.0000101	1730
Missense in Polyphen		34	46.037	0.73854		493
Synonymous	-0.528	82	76.1	1.08	0.00000511	610
Loss of Function	1.22	5	8.93	0.560	3.81e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000600	0.000598
Finnish	0.0000495	0.0000462
European (Non-Finnish)	0.0000367	0.0000352
Middle Eastern	0.000600	0.000598
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor for transcobalamin saturated with cobalamin (TCbl) (PubMed:18779389). Plays an important role in cobalamin uptake (PubMed:18779389, PubMed:20524213). Plasma membrane protein that is expressed on follicular dendritic cells (FDC) and mediates interaction with germinal center B cells (PubMed:10727470). Functions as costimulator to promote B cell responses to antigenic stimuli; promotes B cell differentiation and proliferation (PubMed:10727470, PubMed:11418631). Germinal center-B (GC-B) cells differentiate into memory B-cells and plasma cells (PC) through interaction with T-cells and follicular dendritic cells (FDC) (PubMed:11418631). CD320 augments the proliferation of PC precursors generated by IL-10 (PubMed:11418631). {ECO:0000269|PubMed:10727470, ECO:0000269|PubMed:11418631, ECO:0000269|PubMed:18779389, ECO:0000269|PubMed:20524213}.;
Pathway: Cobalamin (Cbl, vitamin B12) transport and metabolism;Metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

pRec: 0.191

Intolerance Scores

loftool: 0.125
rvis_EVS: 0
rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

pHI: 0.0540
hipred: N
hipred_score: 0.146
ghis: 0.392

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.614

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cd320
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; immune system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: cobalamin metabolic process;regulation of signaling receptor activity;cobalamin transport;regulation of vitamin metabolic process;positive regulation of B cell proliferation;B cell costimulation
Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;endosome membrane;membrane
Molecular function: calcium ion binding;protein binding;growth factor activity;cobalamin-transporting ATPase activity;cobalamin binding