Genetic rare variants and phenotype
| Case | TBX4 nucleotide and protein variant | Genomic position (Hg19; Chr17)# | Putative mechanism and consequence | Genotype and inheritance | ExAC allele frequency, CADD score | ACMG classification | Skeletal anomalies | Other anomalies | Neurological and psychomotor deficits |
| 1 | CNV | 17q23.1q23.2(58 078 171–60 316 749)x1 | Gene deletion haploinsufficiency | Heterozygous De novo | n/a | Pathogenic (ClinGen) | Not known | Hypothyroidism, cortisol deficiency | Hypertonia |
| 2 | CNV | 17q22q23.2(56 623 275–60 285 107)x1 | Gene deletion haploinsufficiency | Heterozygous Not known | n/a | Likely pathogenic (ClinVar) | Facial dysmorphism, foot anomaly, not known | ASD, omphalocele | Developmental delay, seizures, nystagmus |
| 3 | CNV | 17q23.1q23.2(57 972 342–60 472 864)x1 | Gene deletion haploinsufficiency | Heterozygous Not known | n/a | Likely pathogenic (ClinGen) | Joint contractures, foot anomaly | ASD | Mild developmental delay, hearing loss, two-vessel cord, vesicoureteral reflux |
| 4 | CNV | 17q23.1(58 313 766–60 315 220)x1 | Gene deletion haploinsufficiency | Heterozygous Not known | n/a | Likely pathogenic (ClinGen) | Foot anomaly | PDA (ligation at 4 years) | Mild developmental delay |
| 5 | CNV | 17q23.1q23.2 (57 992 012–60 330 998)x1 | Gene deletion haploinsufficiency | Heterozygous Not known | n/a | Likely pathogenic (ClinGen) | SPS, foot anomaly | PDA, ASD, VSD | Developmental delay, nystagmus |
| 6 | CNV | 17q22q23.2(56 429 075–60 181 763)x1 | Gene deletion haploinsufficiency | Heterozygous Not known | n/a | Likely pathogenic | Club foot | ASD, gastrostomy | Microcephaly, hearing loss, esotropia, nystagmus, severe developmental delay |
| 7 | c.251_delG p.(Gly84Alafs*4) | 59 534 962 | Indel Frameshift Loss of function | Heterozygous De novo | ExAC AF: 0 | Pathogenic | Not known | Transient PDA, failure to thrive, Meckel diverticulum | Developmental delay |
| 8 | c.847dupC p.(Gln283Profs*103) | 59 557 506 | Indel Frameshift Loss of function | Heterozygous Not known | ExAC AF: 0 | Likely pathogenic | Not known | No | |
| 9 | c.146delG p.(Gly49Aspfs*39) | 59 533 997 | Indel Frameshift Loss of function | Heterozygous Not known | ExAC AF: 0 | Likely pathogenic | Not known | ASD, obstructive apnoea | No |
| 10 | c.538_547delCCCTTTGGCC p.(Pro180Ilefs*45) | 59 545 007–59 545 016 | Indel Frameshift Loss of function | Heterozygous Not known | ExAC AF: 0 | Likely pathogenic (ClinVar) | SPS, foot anomaly | No | |
| 11 | c.1112–1113insC p.(Pro371Profs*15) | 59 560 348–59 560 349 | Indel Frameshift Loss of function | Heterozygous Not known | ExAC AF: 0 | Likely pathogenic (ClinVar) | Foot anomaly | PDA | No |
| 12 | c.1054C>T p.(Arg352*) | 59 560 290 | Nonsense AA substitution Loss of function | Heterozygous Heritable: (M) c.1054C>T with SPS | ExAC AF: 0 | Likely pathogenic | SPS, pelvis and foot anomaly | ASD, ILD | No |
| 13¶ | c.1018C>T p.(Arg340*) | 59 557 677 | Nonsense AA substitution Loss of function | Heterozygous Heritable: both siblings carrying p.(Arg340*); parents not tested | ExAC AF: 0 | Likely pathogenic | No | Transient PDA and PFO, ILD | No |
| 14¶ | c.1018C>T p.(Arg340*) | 59 557 677 | Nonsense AA substitution Loss of function | Heterozygous Heritable: both siblings carrying p.(Arg340*); parents not tested | ExAC AF: 0 | Likely pathogenic | No | Transient PFO and PDA, ILD | Unknown |
| 15 | c.792-1G>C | 59 557 450 | Splice site AA substitution Loss of function | Heterozygous Heritable: (M) c.792-1G>C with SPS, PH, ILD | ExAC AF: 0 | Likely pathogenic | Foot anomaly | Mandibular angioma | No |
| 16 | c.702+1G>A | 59 556 141 | Splice site AA substitution Loss of function | Heterozygous Heritable: (M) c.702+1G>A | ExAC AF: 0 | Likely pathogenic (ClinVar) | Not known | No | No |
| 17 | c.316G>A p.(Gly106Ser) | 59 534 214 | Missense AA substitution | Heterozygous De novo | ExAC AF: 0.000008236 CADD: 11.0 P2: 1.000 | Likely pathogenic | SPS, pelvis and foot scoliosis | PDA, short stature, angiofibromas, keratoconus | ADHD, autism |
| 18 | c.557T>G p.(Leu186Arg) | 59 555 995 | Missense AA substitution | Heterozygous Heritable: two siblings carrying p.(Leu186Arg), with SPS | ExAC AF: 0 CADD: 28.8 P2: 1.000 | Likely pathogenic (ClinVar) | Pelvis, vertebral and foot anomaly | ASD, PDA, short stature, facial dysmorphism (long philtrum, hypertelorism) | Moderate developmental delay, hypotonia |
| 19 | c.652G>A p.(Val218Met) | 59 556 090 | Missense AA substitution | Heterozygous Not tested | ExAC AF: 0.0001153 CADD: 24.2 P2: 0.635 | Likely pathogenic | No | PFO, short stature, hearing loss | Microcephaly |
TBX4: T-box transcription factor 4; Hg19: Homo sapiens genome assembly GRCh37; Chr17: chromosome 17; ExAC: Exome Aggregation Consortium; CADD: Combined Annotation Dependent Depletion; ACMG: American College of Medical Genetics; CNV: copy number variant; n/a: not available; ASD: atrial septal defect; PDA: patent ductus arteriosus; SPS: small patella syndrome; VSD: ventricular septal defect; AF: allele frequency; AA: amino acid; M: mother; ILD: interstitial lung disease; PFO: patent foramen ovale; PH: pulmonary hypertension; P2: PolyPhen2; ADHD: attention deficit hyperactivity disorder. #: genomic annotations were based on NC_000017.11: homo sapiens chromosome 17, GRCh38.p7 primary assembly; transcript sequence NM_001321120.1; protein sequence NP_001308049.1; ¶: siblings.