CD164

Chr 6AD

CD164 molecule

Also known as: DFNA66, MGC-24, MGC-24v, MUC-24, endolyn

NCBI Gene: 8763ENSG00000135535UniProt: Q04900

This gene encodes a transmembrane sialomucin and cell adhesion molecule that regulates the proliferation, adhesion and migration of hematopoietic progenitor cells. The encoded protein also interacts with the C-X-C chemokine receptor type 4 and may regulate muscle development. Elevated expression of this gene has been observed in human patients with Sezary syndrome, a type of blood cancer, and a mutation in this gene may be associated with impaired hearing. [provided by RefSeq, Oct 2016]

Primary Disease Associations & Inheritance

?Deafness, autosomal dominant 66MIM #616969
AD
159
ClinVar variants
19
Pathogenic / LP
0.49
pLI score
0
Active trials
Clinical Summary— CD164
🧬
Gene-Disease Validity (ClinGen)
autosomal dominant nonsyndromic hearing loss · ADModerate

Moderate evidence — consider for supplementary testing

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.19) despite low pLI — interpret in context.
📋
ClinVar Variants
19 Pathogenic / Likely Pathogenic· 60 VUS of 159 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.61LOEUF
pLI 0.489
Z-score 2.39
OE 0.19 (0.08–0.61)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.26Z-score
OE missense 1.07 (0.92–1.26)
106 obs / 98.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.19 (0.08–0.61)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.07 (0.92–1.26)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.07
0≤1.21.6
LoF obs/exp: 2 / 10.3Missense obs/exp: 106 / 98.8Syn Z: -0.36

ClinVar Variant Classifications

159 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
VUS60
Likely Benign48
Benign31
Conflicting1
19
Pathogenic
60
VUS
48
Likely Benign
31
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
19
0
19
Likely Pathogenic
0
0
0
0
0
VUS
0
50
10
0
60
Likely Benign
0
10
24
14
48
Benign
0
0
29
2
31
Conflicting
—1
Total0608216159

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CD164 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
CD164 ANTIGEN; CD164
MIM #603356 · *

?Deafness, autosomal dominant 66

MIM #616969

Molecular basis of disorder known

Autosomal dominant
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Deciphering the Molecular Characteristics of Human Idiopathic Nonobstructive Azoospermia from the Perspective of Germ Cells.
Chen Y et al.·Adv Sci (Weinh)
2023
Cellular endosomal potassium ion flux regulates arenavirus uncoating during virus entry.
Shaw AB et al.·mBio
2024
Sézary syndrome: old enigmas, new targets.
Nicolay JP et al.·J Dtsch Dermatol Ges
2016Review
CD164 promotes tumor progression and predicts the poor prognosis of bladder cancer.
Zhang XG et al.·Cancer Med
2018
Genome-Wide Knockout Screen Identifies Human Sialomucin CD164 as an Essential Entry Factor for Lymphocytic Choriomeningitis Virus.
Liu J et al.·mBio
2022
LncRNA PTAR activates the progression of bladder cancer by modulating miR-299-3p/CD164 axis.
Han Z et al.·Pathol Res Pract
2022
Update on CD164 and LMX1A genes to strengthen their causative role in autosomal dominant hearing loss.
Oziębło D et al.·Hum Genet
2022
CD164 and FCRL3 are highly expressed on CD4+CD26- T cells in Sézary syndrome patients.
Wysocka M et al.·J Invest Dermatol
2014Cohort
Long non-coding RNA LINC00152/miR-613/CD164 axis regulates cell proliferation, apoptosis, migration and invasion in glioma via PI3K/AKT pathway.
Zhang L et al.·Neoplasma
2020
Distinctiveness of Femoral and Acetabular Mesenchymal Stem and Progenitor Populations in Patients with Primary and Secondary Hip Osteoarthritis Due to Developmental Dysplasia.
Plečko M et al.·Int J Mol Sci
2024Cohort
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools