MR feasibility tier: A — Published pQTL-MR estimates exist for this protein (retrieved below - not computed here).
| Outcome | beta | se | p | method | nSNP | cis/trans | coloc |
|---|---|---|---|---|---|---|---|
| Total cholesterol | -0.0397 | 0.00516 | 1.36e-14 | Wald ratio | 1 | cis | 0.998 |
| LDL cholesterol | -0.0358 | 0.00541 | 3.62e-11 | Wald ratio | 1 | cis | 0.998 |
| Forced vital capacity (FVC) | -0.0191 | 0.003 | 2.27e-10 | Wald ratio | 1 | cis | 0.813 |
| Body mass index (BMI) | 0.0204 | 0.00366 | 2.59e-08 | Wald ratio | 1 | cis | 0.998 |
| Forced expiratory volume in 1-second (FEV1) | -0.0174 | 0.00317 | 4.22e-08 | Wald ratio | 1 | cis | 0.288 |
| Height | 0.0232 | 0.00438 | 1.20e-07 | Wald ratio | 1 | cis | 0.0218 |
| Sleep duration | 0.0137 | 0.00286 | 1.57e-06 | Wald ratio | 1 | cis | NA |
| Weight | 0.0153 | 0.00323 | 2.29e-06 | Wald ratio | 1 | cis | NA |
| Potassium in urine | 0.0171 | 0.00372 | 4.35e-06 | Wald ratio | 1 | cis | NA |
| Fasting insulin | 0.0168 | 0.00438 | 1.32e-04 | Wald ratio | 1 | cis | NA |
| Body fat | 0.0245 | 0.0067 | 2.58e-04 | Wald ratio | 1 | cis | NA |
| Diastolic blood pressure automated reading | 0.0131 | 0.00374 | 4.66e-04 | Wald ratio | 1 | cis | NA |
| …and 123 more outcomes (see JSON) |
No prot-* pQTL GWAS dataset found for this protein (matched by UniProt accession and symbol).
27 association rows across 22 traits (25 genome-wide significant rows). Associations are loci, not causal claims; the mapped gene at a locus is not necessarily the effector gene.
| Trait | best p | lead SNP | n assoc | study | MR status |
|---|---|---|---|---|---|
| Lactase-phlorizin hydrolase levels (LCT.9017.58.3) | 2e-69 | rs1030766 | 1 | GCST90241728 | no MR -> candidate analysis |
| white blood cell count (WBC, maximum, inv-norm transformed) | 9e-36 | rs35940156 | 1 | GCST90480723 | no MR -> candidate analysis |
| DARS1 protein levels | 7e-20 | rs2304371 | 1 | GCST90468947 | no MR -> candidate analysis |
| Aspartate–tRNA ligase, cytoplasmic levels | 8e-19 | rs2304371 | 1 | GCST90246480 | no MR -> candidate analysis |
| Neutrophil count | 1e-15 | rs370868556 | 2 | GCST90002398 | no MR -> candidate analysis |
| Cholesterol esters in very large HDL | 6e-14 | rs3769012 | 1 | GCST90501296 | no MR -> candidate analysis |
| Physical function (baseline) | 9e-14 | rs56064699 | 1 | GCST90565837 | no MR -> candidate analysis |
| Cholesterol levels in very large HDL | 2e-13 | rs3769012 | 1 | GCST90501294 | no MR -> candidate analysis |
| Plasmacytoid Dendritic Cell Absolute Count | 2e-13 | rs2164210 | 1 | GCST90001460 | no MR -> candidate analysis |
| Cholesterol in Large HDL | 6e-13 | rs767569332 | 1 | GCST90501134 | no MR -> candidate analysis |
| Cholesteryl Esters in Large HDL | 8e-13 | rs767569332 | 1 | GCST90501136 | no MR -> candidate analysis |
| White blood cell count | 2e-12 | rs35837297 | 5 | GCST009683 | no MR -> candidate analysis |
| …and 10 more traits (see JSON) |
Top diseases by Open Targets association (of 846 total). Associations are loci, not causal claims. The causal-status column is a four-state triage per pair: established (curated) = a curated clinical assertion exists (ClinGen/G2P/GEL/Orphanet/ClinVar — any validity level, MR adds little); exploratory rare-variant signal = ExWAS burden evidence without curation — a candidate NEW gene-disease relationship; common-variant locus = GWAS signal, classic pQTL-MR territory; multi-layer = burden+GWAS together, an allelic-series candidate (the strongest causal setup). Burden estimand is carrier-vs-noncarrier, not per-SD MR.
| Disease | genetic assoc. | burden (ExWAS) | causal status | MR status |
|---|---|---|---|---|
| congenital lactase deficiency | 0.805 | — | established (curated) | no MR -> candidate analysis |
| obesity disorder | 0.587 | — | common-variant locus | no MR -> candidate analysis |
| lactose intolerance | 0.512 | — | common-variant locus | no MR -> candidate analysis |
| morbid obesity | 0.494 | — | common-variant locus | no MR -> candidate analysis |
| sleep disorder | 0.435 | — | common-variant locus | MR: beta=0.052, p=0.252 (cis) |
| Sjogren syndrome | 0.427 | — | common-variant locus | no MR -> candidate analysis |
| metabolic syndrome | 0.413 | — | common-variant locus | no MR -> candidate analysis |
| cutaneous lupus erythematosus | 0.409 | — | common-variant locus | no MR -> candidate analysis |
| nervous system disorder | 0.385 | — | common-variant locus | no MR -> candidate analysis |
| polycystic ovary syndrome | 0.363 | — | common-variant locus | no MR -> candidate analysis |
| hereditary disease | 0.319 | — | established (curated) | no MR -> candidate analysis |
| essential tremor | 0.306 | — | common-variant locus | no MR -> candidate analysis |
| Menorrhagia | 0.251 | — | common-variant locus | no MR -> candidate analysis |
| Oligomenorrhea | 0.251 | — | common-variant locus | no MR -> candidate analysis |
| Polymenorrhea | 0.251 | — | common-variant locus | no MR -> candidate analysis |
Of the 15 rows above, 14 have no MR estimate in this resource. Across all retrieved diseases for this gene: 0 exploratory rare-variant signal(s), 0 multi-layer (allelic-series candidate) pair(s). Final triage still belongs to a statistical geneticist.
| Layer | Result |
|---|---|
| ChEMBL druggability | 0 known modulators (Lactase/phlorizin hydrolase) |
| gnomAD constraint | pLI=1.8e-11, LOEUF=0.62 — LoF-tolerant |
| GWAS Catalog | 64 unique SNPs / 128 rows |
| ClinVar | 1007 records; 5 pathogenic in sample of 30 |
| PharmGKB/ClinPGx | no annotations |
phenome — Top 30 of 846 associated diseases by overall score. genetic_association aggregates GWAS common-variant AND rare-variant evidence. These are ASSOCIATIONS (loci), not causal claims.chembl — ChEMBL target matched by text search on ‘LCT’ and resolved to ‘Lactase/phlorizin hydrolase’ — confirm this is the intended target.clinvar — Pathogenic count is over the 30 record(s) retrieved, NOT over all 1007 ClinVar records for this gene; it is a sample, not a rate.pharmgkb — No PharmGKB/ClinPGx clinical annotations (gene may not be a pharmacogene).gwas_traits — Top 20 of 22 traits by best p-value, aggregated from 27 association rows. These are GWAS ASSOCIATIONS (loci), not causal claims; mapped genes at a locus are not necessarily the effector gene.uniprot: https://www.uniprot.org/uniprotkb/P09848 — UniProt release 2026_02 (10-June-2026)mr_outcomes: https://epigraphdb.org/pqtl/ — EpiGraphDB pQTL MR (Zheng et al., Nat Genet 2020) — pre-computed two-sample MR; retrieved, not computed by this agent; EpiGraphDB build 1.0, pQTL dataset v3.0phenome: https://platform.opentargets.org/target/ENSG00000115850/associations — Open Targets data release 26.06chembl: https://www.ebi.ac.uk/chembl/target_report_card/CHEMBL1075131/ — ChEMBL_37 (released 2026-05-01)gnomad: https://gnomad.broadinstitute.org/gene/LCT — gnomAD constraint via GraphQL API (reference genome GRCh38)gwas: https://www.ebi.ac.uk/gwas/genes/LCT — GWAS Catalog REST (live; release not exposed by this endpoint)clinvar: https://www.ncbi.nlm.nih.gov/clinvar/?term=LCT%5Bgene%5D — ClinVar build Build260809-1055.1gwas_traits: https://www.ebi.ac.uk/gwas/genes/LCT — GWAS Catalog search API (live; release not exposed)