LHX4

Chr 1AD

LIM homeobox 4

Also known as: CPHD4

NCBI Gene: 89884ENSG00000121454UniProt: Q969G2OMIM: 602146

This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor involved in the control of differentiation and development of the pituitary gland. Mutations in this gene cause combined pituitary hormone deficiency 4. [provided by RefSeq, Dec 2010]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Pituitary hormone deficiency, combined, 4MIM #262700
AD

Clinical highlights

Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
13
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.69
LOEUF
LOF*
Mechanism· G2P
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.69LOEUF
pLI 0.018
Z-score 2.51
OE 0.35 (0.19–0.69)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.67Z-score
OE missense 0.88 (0.78–0.98)
205 obs / 233.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.35 (0.19–0.69)
0≤0.351.4
Missense OE?0.88 (0.78–0.98)
0≤0.61.4
Synonymous OE?1.06
0≤1.21.6
LoF obs/exp: 6 / 17.3Missense obs/exp: 205 / 233.9Syn Z: -0.48

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

LHX4 · 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.

Search ClinicalTrials.gov →

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