| Literature DB >> 35782384 |
Amjad Khan1,2, Lucia Pia Bruno2,3, Fadhel Alomar4, Muhammad Umair5,6, Anna Maria Pinto7, Abid Ali Khan8, Alamzeb Khan9, Alessandra Fabbiani2,3, Kristina Zguro3, Simone Furini3, Maria Antonietta Mencarelli7, Alessandra Renieri2,3,7, Sara Resciniti2,3, Karla A Peña-Guerra10, Francisco J Guzmán-Vega10, Stefan T Arold10,11, Francesca Ariani2,3,7, Shahid Niaz Khan12.
Abstract
Whole exome sequencing has provided significant opportunities to discover novel candidate genes for intellectual disability and autism spectrum disorders. Variants in the spectrin genes SPTAN1, SPTBN1, SPTBN2, and SPTBN4 have been associated with neurological disorders; however, SPTBN5 gene-variants have not been associated with any human disorder. This is the first report that associates SPTBN5 gene variants (ENSG00000137877: c.266A>C; p.His89Pro, c.9784G>A; p.Glu3262Lys, c.933C>G; p.Tyr311Ter, and c.8809A>T; p.Asn2937Tyr) causing neurodevelopmental phenotypes in four different families. The SPTBN5-associated clinical traits in our patients include intellectual disability (mild to severe), aggressive tendencies, accompanied by variable features such as craniofacial and physical dysmorphisms, autistic behavior, and gastroesophageal reflux. We also provide a review of the existing literature related to other spectrin genes, which highlights clinical features partially overlapping with SPTBN5.Entities:
Keywords: SPTBN5; heterozygous mutation; intellectual disability (ID); protein modeling 3; whole exome sequencing (WES)
Year: 2022 PMID: 35782384 PMCID: PMC9248767 DOI: 10.3389/fnmol.2022.877258
Source DB: PubMed Journal: Front Mol Neurosci ISSN: 1662-5099 Impact factor: 6.261
Figure 1(A) Representing pedigrees of all the four families (A–D). (B) Showing Sanger sequencing electro-grams of all the four families. (C) Conservation analysis of the mutations identified in the present studies along different species. (D) Structural models of the CH1 domain containing the His89Pro mutation, and the spectrin repeats containing the Asn2937Tyr and Glu3262Lys mutations. Three 1,000 segments containing the residues of interest were modeled with AlphaFold, and are shown in the bottom as cartoons, colored by pLDDT score. Residues with pLDDT <50 are colored red, representing regions with low confidence, and residues with pLDDT>90 are blue, showing high-confidence segments. The top insets show a zoom into the local region of each mutated residue (shown as blue sticks), and the comparison between the wild-type and mutated states. The residues predicted to interact with His89 are shown as gray sticks. (E) Exon organization of SPTBN5. Boxes are exons. Lines connecting the boxes are introns. Filled boxes are coding sequence, and empty, unfilled boxes are UTR (UnTranslated Region). Adapted from Ensembl (release 105) (Howe et al., 2021).
Clinical features of affected subjects from families A–D.
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| Pedigree ID | II:3 | II:2 | II:3 | II:3 |
| Nationality | Pakistani | Italian | Italian | Italian |
| Gender | Male | Female | Male | Female |
| Current age (Years) | 11 yrs | 15 yrs | 14 yrs | 7 yrs |
| Family history | Sporadic | Familial | Sporadic | Familial |
| Disease onset (years) | First year of life | First year of life | First year of life | First year of life |
| Consanguinity | No | No | No | No |
| Gestation weeks (weeks) | 38 | 39 | 38 | 38 |
| Pregnancy event | Uneventful | Uneventful | Uneventful | Uneventful |
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| Developmental delay | + | + | + | + |
| Language impairment | + | + | + | |
| Learning disability | + | + | + | + |
| Sleep disorder | + | + | + | + |
| Head circumference | 49cm | 50.5 cm | 46.5 cm | – |
| Height | 52.1 cm | 144.5 cm | 150.5 cm | 97 cm |
| Weight | 45.9 kg | 35 kg | 34 kg | 15 kg |
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| Low set ears | + | – | – | – |
| Nasal bridge | Broad | Broad | Depressed | Broad |
| Strabismus | + | – | – | – |
| Facial expression | Triangular | Triangular | Triangular | – |
| Thin upper lip | + | + | + | + |
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| Hands | Bilateral clinodactyly of the 5th little finger | Arachnodactyly, fusiforme fingers of the hands | Bilateral clinodactyly of 4th and 5th fingers of hands | Bilateral clinodactyly of 4th and 5th fingers of hands |
| Feet | Brachydactyly of the feet | Fusiforme fingers of the feet | Bilateral clinodactyly of 4th and 5th fingers of the feet | Bilateral clinodactyly of 4th and 5th fingers of hands |
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| Impairment social interaction | + | + | + | + |
| Feeding difficulty | + | + | – | + |
| Agression/hyperactivity | + | + | + | + |
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| Intellectual disability | + | + | + | + |
| Anxiety/psychiatric | + | + | + | + |
| Seizure | + | + | + | – |
| Amnesia | + | + | + | + |
| Feeding difficulty | + | + | + | + |
| Karyotype | Normal | Normal | Normal | Normal |
+, present; −, absent.
In silico prediction analysis of SPTBN5 variants in the present families.
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| Chromosome location | 15q15.1 | |||
| MIM number | 605916 | |||
| Ensemble ID | ENSG00000137877 | |||
| Total exon | 68 | |||
| cDNA change | c.266A>C | c.9784G>A | c.933C>G | c.8809A>T |
| Protien change | p.His89Pro | p.Glu3262Lys | p.Tyr311Ter | p.Asn2937Tyr |
| Variant exonic location | Exon 3 | Exon 58 | Exon 7 | 53 |
| Variant chromosome location | Chr15:42185210 | Chr15:41853778 | Chr15:41886322 | Chr15: 41856598 |
| Variant type | Non synonymous | Non synonymous | Non synonymous | Non synonymous |
| SIFT | 0.226/Tolerable | 0.127/Tolerable | – | 0.023/Damaging |
| Polyphen-2_HDIV | 0.998/Probably_damaging | 0.003/Benign | – | 0.989/Probably_damaging |
| Polyphen-2_HVAR | 0.939/Probably_damaging | 0.014/Benign | – | 0.832/Possibly_damaging |
| FATHMM | −3.54/ Damaging | 0.73/ Tolerable | – | 0.75/Tolerable |
| Mutation taster | 1.000/Polymorphism | 0.983/Polymorphism | 1/Disease_causing | 0.959/Disease_causing |
| PROVEAN | −5.45/Damaging | 0.25/Tolerable | – | −4.54/Damaging |
| MetaSVM | 0.088/Damaging | −1.014/Tolerable | – | −0.633/Tolerable |
| CADD | 21.2/Damaging | 22.5/Damaging | 35/Damaging | 26.6/Damaging |
| FATHMM_MKL | 0.559/Damaging | 0.513/Damaging | 0.449/Tolerable | 0.990/Damaging |
| GERP++ | 2.82/Conserved | 1.48/conserved | −0.984/Nonconserved | 5.01/Conserved |
| GnomAD_exome All | 0.000004124 | 0.0001 | 0.000008175 | 0.0045 |