GENE REFERENCE / HGNC:10848

SHH

sonic hedgehog signaling molecule

protein-coding gene7q36.3Gene information

What does this gene do?

The SHH gene provides instructions for making a protein called Sonic Hedgehog. This protein functions as a chemical signal that is essential for embryonic development. Sonic Hedgehog plays a role in cell growth, cell specialization, and the normal shaping (patterning) of the body. This protein is important for development of the brain and spinal cord (central nervous system), eyes, limbs, and many other parts of the body.

Sonic Hedgehog is necessary for the development of the front part of the brain (forebrain). This signaling protein helps establish the line that separates the right and left sides of the forebrain (the midline). Specifically, Sonic Hedgehog establishes the midline for the underside (ventral surface) of the forebrain. Sonic Hedgehog and other signaling proteins are needed to form the right and left halves (hemispheres) of the brain.

Sonic Hedgehog also has an important role in the formation of the eyes. During early development, the cells that develop into the eyes form a single structure called the eye field. This structure is located in the center of the developing face. Sonic hedgehog signaling causes the eye field to separate into two distinct eyes.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-09-30. Source review: 2010-09.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
holoprosencephaly 3MONDO:0007733 · Evaluated 2026-08-04	Autosomal dominant	DefinitiveBrain Malformations Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 805
Submissions for variants in or overlapping this gene: 1,051
Submissions explicitly reporting this gene: 912
Alleles reported pathogenic / likely pathogenic: 133
VariationIDs with uncertain significance: 346
VariationIDs with conflicting classifications: 21

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about SHH?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 133 alleles in SHH reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in SHH.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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