Holt-Oram syndrome, also known as atrio-digital syndrome, is a rare autosomal dominant genetic disorder primarily characterized by upper limb malformations and congenital heart defects, associated with mutations in the TBX5 gene. Diagnosis is typically based on clinical presentation, and the prognosis for affected individuals is closely related to the severity of cardiac involvement. Our study aims to highlight some key features of Holt-Oram syndrome to improve the level of clinical diagnosis. We collected 11 patients with clinical features strongly suggestive of Holt-Oram Syndrome at the First Affiliated Hospital of Tsinghua University from January 2010 to January 2025. These patients exhibited both limb malformations and cardiac abnormalities. We then analyzed the characteristics of their diseases. The skeletal abnormalities and cardiac defects presented in diverse forms among the 11 patients. Among the congenital heart diseases, atrial septal defect (ASD) was the most common, accounting for 80% of cases. However, some patients presented with severe conditions such as tetralogy of Fallot or Ebstein's anomaly. Regarding upper limb malformations, the most frequent finding was triphalangeal thumb (8/10 patients), but thumb hypoplasia or aplasia and radial bone abnormalities were also observed. The predominant cardiac structural abnormality in this group of patients was atrial septal defect. Upper limb malformations were predominantly characterized by polydactyly or syndactyly. However, arrhythmias appeared to be mainly supraventricular tachycardia, and upper limb involvement did not seem to show a clear left-sided predominance. The prognosis following cardiac corrective surgery was favorable. Nevertheless, for this condition, emphasis should be placed on prevention. SALL1-related Townes-Brocks syndrome (SALL1-TBS) is characterized by the triad of imperforate anus or anal stenosis, dysplastic ears (overfolded superior helices and preauricular tags; frequently associated with sensorineural and/or conductive hearing impairment), and thumb malformations (duplication of the thumb [preaxial polydactyly], triphalangeal thumbs, and, rarely, hypoplasia of the thumbs) without hypoplasia of the radius. Impaired kidney function, including end-stage kidney disease (ESKD), may occur with or without structural abnormalities (mild malrotation, ectopia, horseshoe kidney, renal hypoplasia, polycystic kidneys, vesicoureteral reflux). Foot malformations (flat feet, overlapping toes) and genitourinary malformations are common. Congenital heart disease occurs in 15% of affected individuals. Developmental delay and/or learning difficulties occur in approximately 15% of affected individuals. Rare features include growth deficiency, Duane anomaly, iris coloboma, and Chiari I malformation. The diagnosis of SALL1-TBS is established in a proband with characteristic clinical findings and a heterozygous pathogenic variant in SALL1 identified by molecular genetic testing. Treatment of manifestations: Immediate surgical intervention for imperforate anus; stool softeners, prokinetics, osmotic agents, or laxatives as needed for constipation; standard treatment of gastroesophageal reflux; early treatment of hearing loss; surgery for severe malformations of the hands; hemodialysis and possibly kidney transplantation for ESKD; management of genitourinary anomalies per urologist or gynecologist; surgery or medical treatment by cardiologist for congenital heart defects; developmental and educational support as needed; neuropsychiatric management as needed for behavioral issues; growth hormone therapy for those with growth hormone deficiency; management of ocular issues per ophthalmologist. Surveillance: Assess for constipation and assess growth and thyroid function at each visit; annual audiology evaluation; monitor kidney function annually in individuals with and without kidney anomalies, even if kidney function is normal on initial examination; monitor developmental progress, educational needs, and behavioral assessment annually; ophthalmology examination per ophthalmologist. Agents/circumstances to avoid: Medications that cause renal or otic toxicity. Evaluation of relatives at risk: Clarify the genetic status of apparently asymptomatic older and younger at-risk relatives of an individual with SALL1-TBS in order to identify as early as possible those who would benefit from clinical evaluation and prompt initiation of treatment for kidney disease and other features of SALL1-TBS. Pregnancy management: Consider prenatal cardiac and nephrology evaluations in pregnant women with SALL1-TBS. SALL1-TBS is inherited in an autosomal dominant manner. About 50% of individuals diagnosed with SALL1-TBS have the disorder as the result of a de novo pathogenic variant. Each child of an individual with SALL1-TBS has a 50% chance of inheriting the pathogenic variant. Once the SALL1 pathogenic variant has been identified in an affected family member, prenatal and preimplantation genetic testing are possible. Holt-Oram syndrome (HOS) is characterized by the association of upper-limb defects, congenital heart malformations, and cardiac conduction disease. Upper-limb malformations are usually bilateral/asymmetric, rarely unilateral or bilateral/symmetric, and affect the radial ray. They can range from thenar hypoplasia, triphalangeal thumb(s), or absent thumb(s) to radial agenesis/hypoplasia to phocomelia. Deformities of the carpal and thenar bones, abnormalities of the shoulders and/or elbows, and vertebral defects can occur. A congenital heart malformation is present in 90% of individuals with HOS and most commonly involves the septum. Atrial septal defect and ventricular septal defect can vary in number, size, and location. Complex congenital heart malformations can also occur in individuals with HOS. Individuals with HOS with or without a congenital heart malformation are at risk for cardiac conduction disease (30%). While individuals may present at birth with sinus bradycardia and first-degree atrioventricular (AV) block, AV block can progress unpredictably to a higher grade including complete heart block with and without atrial fibrillation. The clinical diagnosis of HOS is established by the presence in a proband of a preaxial radial ray anomaly and a personal or family history of cardiac septation and/or conduction defects. More than 70% of individuals who meet strict clinical diagnostic criteria have an identifiable heterozygous pathogenic variant in TBX5. Treatment of manifestations: Management involves a multidisciplinary team of specialists in medical genetics, cardiology, orthopedics, and hand surgery. Treatment of upper-limb malformations per orthopedist can include surgery, physical therapy, occupational therapy, and/or prostheses in those with severe limb shortening. Social and psychological support for affected individuals and families; standard treatment for congenital heart malformation per cardiologist and cardiac surgeon; anticoagulants and antibiotic prophylaxis for bacterial endocarditis if recommended by cardiologist; treatment for arrhythmias may require medication, surgery, and/or pacemaker implantation; pharmacologic treatment for individuals with pulmonary hypertension per cardiologist and/or intensivist. Surveillance: Assess limb function and activities of daily living per orthopedist, physical therapist, and/or occupational therapist; annual EKG in those at risk of developing a conduction defect; annual EKG combined with Holter monitor for individuals with known conduction disease; echocardiogram according to the absence/presence of congenital heart defect and history of heart surgery, every five years in the absence of congenital heart defects to assess for rare cardiomyopathy; surveillance in those with pulmonary hypertension per cardiologist and/or intensivist. Agents/circumstances to avoid: Certain medications may be contraindicated in individuals with arrhythmias, cardiomyopathy, and/or pulmonary hypertension. Evaluation of relatives at risk: Presymptomatic diagnosis and treatment is warranted in relatives at risk to identify those who would benefit from appropriate cardiac management. Pregnancy management: Affected women who have not undergone cardiac evaluation should do so prior to pregnancy or as soon as the pregnancy is recognized; those with a known history of a structural cardiac defect or cardiac conduction abnormality should be followed by a cardiologist during pregnancy. HOS is inherited in an autosomal dominant manner. Some individuals diagnosed with HOS have an affected parent; up to 60% of affected individuals represent simplex cases. Significant intrafamilial variability in limb and heart defect severity is observed among affected family members. Offspring of an individual with HOS have a 50% risk for HOS. If the TBX5 pathogenic variant has been identified in an affected family member, prenatal and preimplantation genetic testing are possible. If the pathogenic variant in the family is not known, prenatal ultrasound (US) examination evaluating for characteristic limb and cardiac manifestations is recommended (a normal US examination does not eliminate the possibility of HOS in the fetus).

Aase-Smith syndrome type 2 is a rare genetic disorder that affects erythropoiesis and bone development, causing hypoplastic anemia and abnormalities in the fingers and toes, specifically triphalangeal thumbs. While there is no cure, treatment involves managing symptoms through blood transfusions, surgical intervention, and genetic counselling. A 15-year-old student presented with an unmeasured fever for two months, recurrent lung infections, difficulty in speech, and impaired gait. The patient had multiple congenital malformations including triphalangeal thumbs and a history of mild anemia. Bone marrow biopsy revealed an isolated slowing of erythroid lineage maturation. Radiology studies showed scoliosis, hand deformities, and multiple calcified lesions in the brain. The patient's fever exacerbated, and oxygen saturation deteriorated, necessitating tracheal intubation. Several hours later, the patient passed away.

Genetic variants in the zone of polarizing activity regulatory sequence (ZRS) that induce ectopic expression of the SHH gene have been associated with different ZRS-related phenotypes. We report the first patient with a de novo variant, c.423+4916 T>C, in ZRS (previously classified as a variant of uncertain significance) that causes tibial hemimelia-polysyndactyly-triphalangeal thumb syndrome (THPTTS). A two-month-old male patient presented with bilateral preaxial polydactyly, triphalangeal thumb, and tibial agenesis and was heterozygous for the variant c.423+4916T>C (neither of his parents was a carrier). The findings obtained from the family study were sufficient to reclassify the variant from "uncertain significance" to "likely pathogenic" according to three criteria from the American College of Medical Genetics and Genomics guidelines, as follows: (1) absence of gnomAD, (2) confirmation of paternity and maternity, and (3) strong phenotype-genotype association. In ZRS-associated syndromes, a wide clinical spectrum has been observed, ranging from polydactyly to THPTTS; our patient has the most severe and rare phenotype. We did not perform functional assays. However, the c.423+4916T>C variant is flanked by three variants, which have been proven not only to cause the phenotype but also to increase the expression of SHH. Through all this data gathering, we consider the c.423+4916T>C variant to be causative of THPTTS.

Townes-Brocks syndrome (TBS) is a rare syndrome characterized by triad of anal, ear, and thumb anomalies. Further malformations/anomalies include congenital heart diseases, foot malformations, sensorineural and/or conductive hearing impairment, genitourinary malformations, and anomalies of eye and nervous system. Definitive diagnosis for TBS is confirmed by molecular analysis for mutations in the SALL1 gene. Only one known case of TBS with absent pulmonary valve syndrome (APVS) has been previously described to our knowledge. Here, we report a newborn diagnosed with TBS with APVS and tetralogy of Fallot (TOF) who was found to carry the most common pathogenic SALL1 gene mutation c.826C > T (p.R276X), with its surgical repair and postoperative follow-up. To our knowledge, this is the first genotyped case of TBS from Turkey to date. TBS should be suspected in the presence of ear, anal, and thumb malformations in a neonate. If a patient with TBS and TOF-APVS needs preoperative ventilation within the first months of life, this implies prolonged postoperative intubation and increased risk of mortality.

Herein, we report on a large Polish family presenting with a classical triphalangeal thumb-polysyndactyly syndrome (TPT-PS). This rare congenital limb anomaly is generally caused by microduplications encompassing the Sonic Hedgehog (SHH) limb enhancer, termed the zone of polarizing activity (ZPA) regulatory sequence (ZRS). Recently, a pathogenic variant in the pre-ZRS (pZRS), a conserved sequence located near the ZRS, has been described in a TPT-PS Dutch family. We performed targeted ZRS sequencing, array comparative genomic hybridization, and whole-exome sequencing. Next, we sequenced the recently described pZRS region. Finally, we performed a circular chromatin conformation capture-sequencing (4C-seq) assay on skin fibroblasts of one affected family member and control samples to examine potential alterations in the SHH regulatory domain and functionally characterize the identified variant. We found that all affected individuals shared a recently identified pathogenic point mutation in the pZRS region: NC_000007.14:g.156792782C>G (GRCh38/hg38), which is the same as in the Dutch family. The results of 4C-seq experiments revealed increased interactions within the whole SHH regulatory domain (SHH-LMBR1 TAD) in the patient compared to controls. Our study expands the number of TPT-PS families carrying a pathogenic alteration of the pZRS and underlines the importance of routine pZRS sequencing in the genetic diagnostics of patients with TPT-PS or similar phenotypes. The pathogenic mutation causative for TPT-PS in our patient gave rise to increased interactions within the SHH regulatory domain in yet unknown mechanism. SALL4-related disorders include Duane-radial ray syndrome (DRRS, Okihiro syndrome), acro-renal-ocular syndrome (AROS), and SALL4-related Holt-Oram syndrome (HOS) – three phenotypes previously thought to be distinct entities. DRRS is characterized by uni- or bilateral Duane anomaly and radial ray malformation that can include thenar hypoplasia and/or hypoplasia or aplasia of the thumbs, hypoplasia or aplasia of the radii, shortening and radial deviation of the forearms, triphalangeal thumbs, and duplication of the thumb (preaxial polydactyly). AROS is characterized by radial ray malformations, renal abnormalities (mild malrotation, ectopia, horseshoe kidney, renal hypoplasia, vesicoureteral reflux, bladder diverticula), ocular coloboma, and Duane anomaly. Rarely, pathogenic variants in SALL4 may cause clinically typical HOS (i.e., radial ray malformations and cardiac malformations without additional features). The diagnosis of a SALL4-related disorder is established in a proband with suggestive findings and a heterozygous pathogenic variant in SALL4 identified by molecular genetic testing. Treatment of manifestations: Surgery as needed for strabismus from Duane anomaly, malformations of the forearms, and congenital heart defects; management of renal anomalies per nephrologist and/or urologist; antiarrhythmic medications or pacemaker for those with conduction defects or heart block; cardiologist can assist in determining the need for anticoagulants and antibiotic prophylaxis for bacterial endocarditis; hearing aids as needed; consideration of growth hormone therapy for children with growth deficiency; treatment of pituitary hypoplasia per endocrinologist. Surveillance: Ophthalmologic exam with frequency as recommended by ophthalmologist; monitor renal function in those with renal anomalies, even if renal function is normal initially; periodic renal ultrasound evaluation if renal position anomalies could cause obstruction; periodic echocardiographic surveillance may be recommended for individuals with certain congenital heart defects; in those at risk for conduction defects, EKG at least annually with consideration of annual Holter monitor in those with known conduction defects; at least annual blood counts in those with a history of thrombocytopenia and leukocytosis; audiologic evaluation as needed; assessment of growth and for signs and symptoms of pituitary hypoplasia at each visit. Agents/circumstances to avoid: Drugs affecting the kidney if renal function is impaired, or the inner ear if hearing is impaired; certain medications may be contraindicated in those with arrhythmias. SALL4-related disorders are inherited in an autosomal dominant manner. The proportion of cases caused by a de novo pathogenic variant is approximately 40%-50%. Each child of an individual with a SALL4-related disorder has a 50% chance of inheriting the pathogenic variant. Prenatal testing for a pregnancy at increased risk is possible if the pathogenic variant has been identified in an affected family member.