LY6G5C

Chr 6

lymphocyte antigen 6 family member G5C

Also known as: C6orf20, G5C, LY6G5CA, LY6G5CB, NG33

NCBI Gene: 80741ENSG00000204428UniProt: Q5SRR4

The LY6G5C protein is a GPI-anchored cell surface protein that may function in hematopoietic cell differentiation and belongs to the leukocyte antigen-6 superfamily involved in signal transduction. No disease associations or inheritance patterns have been established for mutations in this gene based on the available information.

ResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.93
Clinical Summary— LY6G5C
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.
📋
ClinVar Variants
9 unique Pathogenic / Likely Pathogenic· 13 VUS of 28 total submissions
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.93LOEUF
pLI 0.405
Z-score 1.68
OE 0.20 (0.07–0.93)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.34Z-score
OE missense 0.59 (0.47–0.75)
49 obs / 83.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.20 (0.07–0.93)
0≤0.351.4
Missense OE0.59 (0.47–0.75)
0≤0.61.4
Synonymous OE0.92
0≤1.21.6
LoF obs/exp: 1 / 5.1Missense obs/exp: 49 / 83.4Syn Z: 0.37
DN
0.6841th %ile
GOF
0.5759th %ile
LOF
0.2582th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

28 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5
Likely Pathogenic4
VUS13
Likely Benign2
5
Pathogenic
4
Likely Pathogenic
13
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
5
0
5
Likely Pathogenic
0
0
4
0
4
VUS
0
9
4
0
13
Likely Benign
0
1
0
1
2
Benign
0
0
0
0
0
Total01013124

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

View in ClinVar →

Protein Context — Lollipop Plot

LY6G5C · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Multilayered Epigenetic Analysis Identifies a Molecular Portrait for Psychological Resilience in Patients With Breast Cancer
Richter C et al.·Biol Psychiatry Glob Open Sci
2025Cohort
Comparative transcriptome analysis in the caput segment of yak and cattleyak epididymis.
Adjei M et al.·Theriogenology
2023
High mRNA expression of LY6 gene family is associated with overall survival outcome in pancreatic ductal adenocarcinoma
Russ E et al.·Oncotarget
2021
Human LY6 gene family: potential tumor-associated antigens and biomarkers of prognosis in uterine corpus endometrial carcinoma
Rathbun LA et al.·Oncotarget
2023
Risk Effects of rs1799945 Polymorphism of the HFE Gene and Intergenic Interactions of GWAS-Significant Loci for Arterial Hypertension in the Caucasian Population of Central Russia
Ivanova T et al.·Int J Mol Sci
2023
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients