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.

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.

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				11	2	13
missense			27	8		35
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3		4
non coding			2	16	23	41
Total	0	0	29	35	26

Variants in CD164

This is a list of pathogenic ClinVar variants found in the CD164 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-109368228-A-G			Benign (Jun 22, 2018)
6-109368318-T-A		CD164-related disorder	Likely benign (Jan 14, 2020)
6-109368478-T-C			Benign (Dec 10, 2018)
6-109368531-G-C			Likely benign (Aug 04, 2020)
6-109368699-C-T			Benign (Dec 12, 2018)
6-109368704-G-T			Benign (Nov 10, 2018)
6-109368842-T-G		not specified	Uncertain significance (May 15, 2024)
6-109368854-C-T			Likely benign (Aug 04, 2023)
6-109368870-C-T		not specified • CD164-related disorder	Likely benign (Oct 26, 2024)
6-109368871-G-A		Autosomal dominant nonsyndromic hearing loss 66	no classifications from unflagged records (Apr 25, 2024)
6-109368874-C-T		not specified	Uncertain significance (Sep 13, 2023)
6-109368882-T-C			Uncertain significance (Sep 19, 2024)
6-109368888-A-T		not specified	Uncertain significance (Dec 28, 2022)
6-109368896-A-C			Likely benign (Jun 29, 2022)
6-109368897-A-G		not specified	Uncertain significance (Oct 26, 2024)
6-109368904-A-G		not specified	Uncertain significance (Jan 24, 2024)
6-109368991-T-C		not specified	Uncertain significance (Jun 26, 2024)
6-109368995-A-C			Likely benign (May 11, 2023)
6-109369029-G-C			Benign (Sep 16, 2024)
6-109369314-G-A			Likely benign (Dec 12, 2018)
6-109370125-T-C			Benign (Dec 12, 2018)
6-109370351-G-GTA			Likely benign (Jun 14, 2018)
6-109370395-A-G			Likely benign (Aug 09, 2022)
6-109370418-A-C			Likely benign (Aug 17, 2023)
6-109370420-T-G		not specified	Uncertain significance (Aug 12, 2024)

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

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