CD164

CD164 molecule, the group of CD molecules

Basic information

Region (hg38): 6:109366514-109382467

Links

ENSG00000135535

∙ NCBI:8763 ∙ OMIM:603356 ∙ HGNC:1632 ∙ Uniprot:Q04900 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

autosomal dominant nonsyndromic hearing loss 66 (Limited), mode of inheritance: AD
autosomal dominant nonsyndromic hearing loss (Supportive), mode of inheritance: AD
autosomal dominant nonsyndromic hearing loss 66 (Limited), mode of inheritance: Unknown
autosomal dominant nonsyndromic hearing loss (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal dominant 66	AD	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	26197441

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD164 gene.

not_provided (59 variants)
not_specified (40 variants)
CD164-related_disorder (9 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Autosomal_dominant_nonsyndromic_hearing_loss_66 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD164 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006016.6. 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				13 clinvar	2 clinvar	15
missense			42 clinvar	8 clinvar		50
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	21	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD164	protein_coding	protein_coding	ENST00000310786	6	16046

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.489	0.507	124558	0	1	124559	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	106	98.8	1.07	0.00000489	1226
Missense in Polyphen		60	60.489	0.99191		750
Synonymous	-0.361	42	39.1	1.07	0.00000204	406
Loss of Function	2.39	2	10.3	0.195	5.85e-7	112

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000546	0.0000546
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Sialomucin that may play a key role in hematopoiesis by facilitating the adhesion of CD34(+) cells to the stroma and by negatively regulating CD34(+)CD38(lo/-) cell proliferation. Modulates the migration of umbilical cord blood CD133+ cells and this is mediated through the CXCL12/CXCR4 axis. May play an important role in prostate cancer metastasis and the infiltration of bone marrow by cancer cells. Promotes myogenesis by enhancing CXCR4-dependent cell motility. Positively regulates myoblast migration and promotes myoblast fusion into myotubes (By similarity). {ECO:0000250|UniProtKB:Q9R0L9, ECO:0000269|PubMed:16859559, ECO:0000269|PubMed:17077324, ECO:0000269|PubMed:9763543}.;
Disease: DISEASE: Deafness, autosomal dominant, 66 (DFNA66) [MIM:616969]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:26197441}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Lysosome - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

pRec: 0.115

Intolerance Scores

loftool: 0.423
rvis_EVS: -0.1
rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

pHI: 0.293
hipred: N
hipred_score: 0.169
ghis: 0.518

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.379

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cd164
Phenotype

Zebrafish Information Network

Gene name: cd164
Affected structure: whole organism
Phenotype tag: abnormal
Phenotype quality: increased curvature

Gene ontology

Biological process: immune response;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;negative regulation of cell adhesion;signal transduction;multicellular organism development;muscle organ development;negative regulation of cell population proliferation;hemopoiesis
Cellular component: extracellular region;lysosome;lysosomal membrane;endosome;plasma membrane;integral component of plasma membrane;endosome membrane;cytoplasmic vesicle
Molecular function: protein binding