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Chromosome 7
Home of CFTR (cystic fibrosis) and the Williams-syndrome critical region.
Schematic of chromosome 7 showing the short (p) and long (q) arms. Arm ratio per GRCh38 - banding schematic.
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Overview
Chromosome 7 accounts for approximately five per cent of the human genome and carries around 989 protein-coding genes. It is a submetacentric chromosome, meaning the centromere sits off-centre so that the short arm (7p) and long arm (7q) differ in length but both arms are substantial in length. Clinically, chromosome 7 is best known for CFTR, mutations in which cause cystic fibrosis, and for the 7q11.23 microdeletion syndrome called Williams-Beuren syndrome. The chromosome also hosts genes central to cancer biology (BRAF, EGFR), cardiovascular electrical signalling (KCNH2), and connective-tissue assembly (COL1A2).
Because chromosome 7 does not participate in sex determination and is not subject to X-inactivation, both copies are fully active in every cell. Pathogenic variants or structural rearrangements on chromosome 7 can therefore manifest in autosomal-dominant or autosomal-recessive patterns depending on the gene and mechanism involved. The mix of single-gene disorders, cancer predisposition syndromes, and microdeletion syndromes makes chromosome 7 a frequent focus in NHS genomic medicine, from newborn bloodspot screening for cystic fibrosis through to cancer panels and chromosomal microarray analysis.
Structure
Like all human chromosomes, chromosome 7 consists of a short arm (7p) and a long arm (7q) joined at the centromere. The centromere of chromosome 7 lies closer to the middle than to either end, producing arms of unequal but substantial length and classifying the chromosome as submetacentric. The p arm extends from the centromere to the telomere at the tip of the short arm, whilst the q arm reaches from the centromere to the opposite telomeric end. Cytogeneticists divide each arm into numbered regions and sub-bands using Giemsa staining patterns, which reveal alternating light and dark bands that reflect differences in DNA compaction and gene density.
At the molecular level, the 159.3 million base pairs of chromosome 7 are wound around histone protein spools to form nucleosomes, the repeating units of chromatin. During most of the cell cycle, chromatin remains relatively loose, allowing gene-regulatory machinery access to DNA. When a cell prepares to divide, chromatin condenses dramatically into the compact X-shaped structure visible under a microscope at metaphase. This packaging ensures that the two sister copies of chromosome 7 can be pulled apart cleanly into daughter cells, maintaining genomic stability across generations.
Video: What is a karyotype?
Notable regions
The 7q31.2 band is home to CFTR, which encodes a chloride channel essential for salt and water balance across epithelial surfaces in the lungs, pancreas, sweat glands, and digestive tract. Pathogenic variants in CFTR disrupt chloride transport, leading to thick, sticky mucus that clogs airways and pancreatic ducts in cystic fibrosis. More than two thousand different variants have been catalogued in CFTR to date, with p.Phe508del (a three-base-pair deletion) being the most common alteration in Northern European populations. The NHS newborn bloodspot screen includes cystic fibrosis, and subsequent sweat testing or CFTR sequencing through regional genetics laboratories confirms the diagnosis.
The 7q11.23 band contains the Williams-Beuren syndrome critical region, a stretch of approximately 1.5 to 1.8 million base pairs that is deleted in individuals with Williams syndrome. This microdeletion typically encompasses 26 to 28 genes, including ELN (elastin) and LIMK1. Loss of one copy of ELN is thought to underlie the cardiovascular features, particularly supravalvular aortic stenosis and generalised arteriopathy, whilst haploinsufficiency of multiple neighbouring genes contributes to the distinctive facial appearance, intellectual disability, and sociable personality profile. Because the deletion arises through non-allelic homologous recombination between flanking low-copy repeats, most cases are de novo rather than inherited. Diagnosis is confirmed by fluorescence in-situ hybridisation or chromosomal microarray, both available through NHS cytogenetics services.
The 7p12.2 region houses EGFR, which encodes the epidermal growth factor receptor, a transmembrane tyrosine kinase that relays growth signals into the cell. Amplification or activating mutations in EGFR are frequent drivers of non-small-cell lung cancer and glioblastoma. In the oncology setting, targeted therapies such as tyrosine-kinase inhibitors are guided by EGFR mutation status detected through tumour genomic profiling, a service increasingly embedded in NHS cancer pathways. Germline variants in EGFR are rare, but somatic alterations in tumours make this locus a major focus of precision oncology.
Notable genes
CFTR is perhaps the most clinically significant gene on chromosome 7. The protein it encodes acts as a gated channel, allowing chloride ions to move out of cells in response to cyclic-AMP signals. When both copies of CFTR carry pathogenic variants, the resulting cystic fibrosis manifests as chronic lung infections, pancreatic insufficiency, male infertility, and elevated sweat chloride. CFTR modulators, a class of therapies that partially restore channel function for certain variants, have transformed outcomes for many patients and are available through NHS specialist centres.
BRAF, located at 7q34, encodes a serine-threonine kinase in the RAS-RAF-MEK-ERK signalling cascade. The p.Val600Glu substitution is found in roughly half of all cutaneous melanomas and in subsets of colorectal cancer, papillary thyroid cancer, and hairy-cell leukaemia. Tumour testing for BRAF mutations informs eligibility for BRAF and MEK inhibitor combinations, which are available through NHS specialist cancer services for advanced melanoma. COL1A2 provides instructions for the alpha-2 chain of type I collagen, the most abundant protein in bone, skin, and tendon. Pathogenic variants cause osteogenesis imperfecta (brittle-bone disease) and certain forms of Ehlers-Danlos syndrome, with clinical pictures ranging from perinatal lethality to milder joint hypermobility. KCNH2 encodes a cardiac potassium channel critical for repolarisation; loss-of-function variants prolong the QT interval on electrocardiogram, raising the risk of life-threatening arrhythmia in long-QT syndrome type 2, whilst rare gain-of-function changes shorten the QT interval. PMS2 is part of the DNA mismatch-repair machinery; bi-allelic pathogenic variants cause constitutional mismatch-repair deficiency syndrome with childhood cancers, and heterozygous variants confer Lynch syndrome predisposition to colorectal and endometrial cancer, though PMS2 assessment is technically challenging because of numerous pseudogenes.
Chromosomal disorders
Williams-Beuren syndrome is the signature microdeletion disorder of chromosome 7. The 7q11.23 deletion arises when the two chromosome 7 homologues misalign during meiosis, and recombination between flanking repeat blocks excises the intervening segment. Children with Williams syndrome typically present with a distinctive facial appearance (broad forehead, short nose, wide mouth), developmental delay, a highly sociable and empathetic personality, and supravalvular aortic stenosis or other cardiovascular anomalies. Growth is often slow, and mild to moderate intellectual disability is common, though language skills may be relatively preserved. Because the deletion is usually de novo, recurrence risk for future siblings is low. Diagnosis rests on chromosomal microarray or FISH, both offered through NHS regional genetics laboratories when clinical features raise suspicion.
Whilst whole-chromosome trisomy or monosomy of chromosome 7 is generally embryonically lethal and rarely seen in liveborn infants, mosaic trisomy 7 has been reported in placental tissue and occasionally in liveborn children with growth restriction and developmental concerns. Uniparental disomy of chromosome 7 (UPD7), in which both copies are inherited from one parent, can occur and may be associated with Silver-Russell syndrome when both copies come from the mother (maternal UPD7), leading to growth restriction and asymmetry. Testing for UPD7 is available in specialist centres when Silver-Russell syndrome is suspected on clinical grounds and methylation studies of chromosome 11 (the primary genetic test for Silver-Russell syndrome) are uninformative. Partial duplications or deletions outside the classic 7q11.23 region are rare but may be detected incidentally on microarray, and their clinical significance is interpreted by comparing the genomic coordinates against databases of known pathogenic copy-number variants.
Prenatal screening & diagnosis
Antenatal ultrasound may identify features suggestive of Williams syndrome, such as cardiac outflow-tract abnormalities or intrauterine growth restriction, prompting referral for foetal echocardiography and detailed anatomy scan. Non-invasive prenatal testing (NIPT) from maternal blood screens for common whole-chromosome aneuploidies (trisomies 13, 18, and 21) but does not routinely detect microdeletions of chromosome 7. When structural anomalies are seen on scan or there is a family history of a chromosome 7 disorder, diagnostic testing via chorionic-villus sampling or amniocentesis can be offered. Chromosomal microarray performed on foetal cells can identify the 7q11.23 deletion, whilst targeted sequencing or deletion-duplication analysis can detect CFTR pathogenic variants if there is a known family history of cystic fibrosis.
Postnatally, the NHS newborn bloodspot screening programme includes cystic fibrosis. Samples are tested for immunoreactive trypsinogen, and elevated levels trigger DNA analysis of common CFTR variants. Infants with two pathogenic variants identified, or one variant plus a persistently raised immunoreactive trypsinogen, are referred to specialist paediatric respiratory teams for sweat testing and clinical confirmation. For other chromosome 7 disorders, diagnosis typically follows clinical recognition: a child with developmental delay, sociable affect, and a heart murmur may prompt chromosomal microarray that reveals the 7q11.23 deletion, whilst a teenager with recurrent fractures after minor trauma may undergo sequencing of COL1A2. Increasingly, exome or genome sequencing through the NHS Genomic Medicine Service returns diagnoses in children with unexplained developmental disorders, and genes on chromosome 7 feature prominently in these panels.
Inheritance & recurrence
Most Williams syndrome cases arise de novo, meaning neither parent carries the 7q11.23 deletion and the recurrence risk for future children is very low (though slightly above the general population baseline because of possible germline mosaicism). If a parent is found to carry the deletion, which occasionally happens in mildly affected or mosaic individuals, the recurrence risk is fifty per cent for each pregnancy, following autosomal-dominant inheritance. For single-gene disorders on chromosome 7, inheritance patterns vary by gene. CFTR follows autosomal-recessive inheritance: two carrier parents each have a one-in-four chance of having an affected child with cystic fibrosis in each pregnancy. Carrier testing and preconception counselling are available through NHS clinical genetics services, particularly when there is a family history. COL1A2 and KCNH2 disorders typically follow autosomal-dominant inheritance, so a parent with osteogenesis imperfecta or long-QT syndrome has a fifty per cent chance of passing the pathogenic variant to each child, though penetrance and expressivity can vary. PMS2-related Lynch syndrome is also autosomal dominant, and cascade testing of at-risk relatives is a key component of cancer-prevention pathways.
When a pathogenic variant or structural abnormality on chromosome 7 is identified in a child, NHS clinical genetics teams offer family counselling to clarify inheritance, estimate recurrence risks, and discuss reproductive options such as preimplantation genetic testing or prenatal diagnosis in future pregnancies. For de-novo events, parents are reassured that the chance of recurrence is low, though the small possibility of germline mosaicism is acknowledged. Tailored risk figures depend on the specific gene, the variant, and the family structure, underscoring the value of expert genetic counselling rather than generic percentage estimates.
Frequently asked questions
What is the most common genetic condition linked to chromosome 7?
Cystic fibrosis, caused by pathogenic variants in the CFTR gene at 7q31.2, is the most prevalent life-limiting autosomal-recessive condition in populations of Northern European ancestry. The NHS newborn bloodspot screen tests every baby for cystic fibrosis, allowing early intervention and monitoring through specialist respiratory centres.
How is Williams syndrome diagnosed, and can it be detected before birth?
Williams syndrome is confirmed by chromosomal microarray or fluorescence in-situ hybridisation, which detect the 7q11.23 microdeletion. Antenatal ultrasound may identify cardiac or growth concerns that prompt foetal echocardiography and, if warranted, invasive testing such as amniocentesis. Because the deletion is usually de novo, routine prenatal screening does not include it, but targeted analysis is available when features are seen on scan.
If both my partner and I are carriers of a CFTR variant, what are our options?
Each pregnancy has a one-in-four chance of resulting in a child with cystic fibrosis, a one-in-two chance of a carrier child, and a one-in-four chance of a child inheriting neither variant. NHS clinical genetics services offer preconception counselling, and options include prenatal diagnosis via chorionic-villus sampling or amniocentesis, or preimplantation genetic testing if in-vitro fertilisation is planned. Your genetics team can discuss which approach suits your circumstances.
Are chromosome 7 disorders usually inherited or do they arise spontaneously?
It depends on the disorder. The 7q11.23 microdeletion causing Williams syndrome is typically de novo, meaning it occurs for the first time in the affected child. In contrast, cystic fibrosis follows autosomal-recessive inheritance, so affected individuals have two carrier parents. Conditions such as long-QT syndrome type 2 (KCNH2) and osteogenesis imperfecta (COL1A2) are often autosomal dominant, so one affected parent can pass the variant to children, though de-novo variants also occur.
Can chromosome 7 abnormalities cause cancer?
Germline pathogenic variants in PMS2 on chromosome 7 raise the risk of colorectal, endometrial, and other cancers as part of Lynch syndrome. Additionally, somatic mutations in BRAF and amplifications of EGFR arise in tumour cells and drive many cancers, particularly melanoma, lung cancer, and glioblastoma. NHS cancer genomic testing increasingly includes these genes to guide targeted therapies, though the mutations in cancer cells are acquired rather than inherited.
Launch-set genes on chromosome 7
Genes on this chromosome that currently have dedicated pages in the library. This list grows as we publish more.