LYZL1

Chr 10

lysozyme like 1

Also known as: KAAG648, LYC2, LYZD1, PRO1278, bA534G20.1

NCBI Gene: 84569ENSG00000120563UniProt: Q6UWQ5

The protein is predicted to function as a lysozyme in the extracellular region, breaking down bacterial cell walls as part of innate immune defense. LYZL1 mutations cause teratozoospermia, characterized by abnormal sperm morphology leading to male infertility. The gene shows low constraint against loss-of-function variants, and the inheritance pattern for this condition has not been clearly established.

Summary from RefSeq
Research Assistant →
0
Active trials
0
Pubs (1 yr)
13
P/LP submissions
0%
P/LP missense
1.73
LOEUF
DN
Mechanism· predicted
Clinical Summary— LYZL1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
13 unique Pathogenic / Likely Pathogenic· 34 VUS of 56 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
1.73LOEUF
pLI 0.000
Z-score -0.10
OE 1.04 (0.62–1.73)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.02Z-score
OE missense 1.01 (0.86–1.18)
112 obs / 111.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.04 (0.62–1.73)
0≤0.351.4
Missense OE1.01 (0.86–1.18)
0≤0.61.4
Synonymous OE1.17
0≤1.21.6
LoF obs/exp: 9 / 8.7Missense obs/exp: 112 / 111.4Syn Z: -0.90
DN
0.6162th %ile
GOF
0.6248th %ile
LOF
0.2776th %ile

The Badonyi & Marsh model scores gain-of-function highest, but genomic evidence most strongly supports dominant-negative as the primary mechanism.

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

56 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic12
Likely Pathogenic1
VUS34
Likely Benign4
Benign3
12
Pathogenic
1
Likely Pathogenic
34
VUS
4
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
12
0
12
Likely Pathogenic
0
0
1
0
1
VUS
0
24
10
0
34
Likely Benign
0
2
1
1
4
Benign
0
0
3
0
3
Total02627154

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

View in ClinVar →

Protein Context — Lollipop Plot

LYZL1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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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 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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