LYPD6B

Chr 2

LY6/PLAUR domain containing 6B

Also known as: CT116, LYPD7

NCBI Gene: 130576ENSG00000150556UniProt: Q8NI32

The protein modulates nicotinic acetylcholine receptor activity in a subtype-specific manner, particularly enhancing sensitivity and altering desensitization of certain receptor combinations. Mutations in LYPD6B cause autosomal recessive intellectual disability with microcephaly and behavioral abnormalities. The gene shows low constraint against loss-of-function variants, consistent with the recessive inheritance pattern observed in affected families.

ResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.13
Clinical Summary— LYPD6B
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
18 unique Pathogenic / Likely Pathogenic· 26 VUS of 63 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.13LOEUF
pLI 0.000
Z-score 1.27
OE 0.60 (0.34–1.13)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.65Z-score
OE missense 0.83 (0.71–0.98)
99 obs / 118.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.60 (0.34–1.13)
0≤0.351.4
Missense OE0.83 (0.71–0.98)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 7 / 11.7Missense obs/exp: 99 / 118.8Syn Z: -0.34
DN
0.6453th %ile
GOF
0.4973th %ile
LOF
0.3259th %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

63 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
Likely Pathogenic1
VUS26
Likely Benign5
17
Pathogenic
1
Likely Pathogenic
26
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
17
0
17
Likely Pathogenic
0
0
1
0
1
VUS
0
22
4
0
26
Likely Benign
0
4
0
1
5
Benign
0
0
0
0
0
Total02622149

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

View in ClinVar →

Protein Context — Lollipop Plot

LYPD6B · 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
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 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