An
Autosomal recessive, X-linked dominant
mode(s) within the
Neurodevelopmental disorders
category
Conflicting classifications of pathogenicity
5
Likely pathogenic
3
Pathogenic
3
Pathogenic/Likely pathogenic
9
Uncertain significance
3
| Variant name | Variant type | GRCH38 location | Germline classification | Molecular consequence | dbSNP_ID | Submitter |
|---|---|---|---|---|---|---|
| NM_001134831.2(AHI1):c.1799_1802del (p.Lys600fs) | Microsatellite | Chr6:135442692 - 135442695 | Pathogenic/Likely pathogenic | Frameshift variant | rs1786504555 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Suma Genomics |
| NM_001134831.2(AHI1):c.1765C>T (p.Arg589Ter) | Single nucleotide variant | Chr6:135447022 | Pathogenic | Nonsense | rs267606641 |
.Lifecell International Pvt. Ltd |
| NM_001174150.2(ARL13B):c.89A>G (p.Asp30Gly) | Single nucleotide variant | Chr3:93995903 | Uncertain significance | Missense variant|5 prime UTR variant|non-coding transcript variant|intron variant | rs2471926773 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_001352754.2(ARMC9):c.879G>A (p.Thr293=) | Single nucleotide variant | Chr2:231240041 | Pathogenic/Likely pathogenic | Synonymous variant|non-coding transcript variant|intron variant | rs766572502 |
.Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS |
| NM_001378615.1(CC2D2A):c.4230G>T (p.Trp1410Cys) | Single nucleotide variant | Chr4:15589595 | Likely pathogenic | Missense variant | rs2475127881 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001378615.1(CC2D2A):c.4088G>T (p.Gly1363Val) | Single nucleotide variant | Chr4:15587838 | Conflicting classifications of pathogenicity | Missense variant | rs762683334 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001378615.1(CC2D2A):c.4555T>G (p.Trp1519Gly) | Single nucleotide variant | Chr4:15599587 | Likely pathogenic | Missense variant | rs1577406415 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_025114.4(CEP290):c.4805C>T (p.Thr1602Met) | Single nucleotide variant | Chr12:88083854 | Conflicting classifications of pathogenicity | Missense variant | rs369451049 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Neuberg Centre For Genomic Medicine, NCGM |
| NM_025114.4(CEP290):c.5745dup (p.Lys1916Ter) | Duplication | Chr12:88071890 - 88071891 | Pathogenic/Likely pathogenic | Nonsense | rs751361090 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_025114.4(CEP290):c.5668G>T (p.Gly1890Ter) | Single nucleotide variant | Chr12:88077263 | Pathogenic/Likely pathogenic | Nonsense | rs137852832 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital .Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Neuberg Centre For Genomic Medicine, NCGM .Suma Genomics |
| NM_001384732.1(CPLANE1):c.6114del (p.Asp2039fs) | Deletion | Chr5:37173812 | Likely pathogenic | Frameshift variant | rs2547674026 |
.Lifecell International Pvt. Ltd |
| NM_001384732.1(CPLANE1):c.3056_3059dup (p.Trp1020fs) | Microsatellite | Chr5:37206286 - 37206287 | Pathogenic/Likely pathogenic | Frameshift variant | rs769934551 |
.Pediatrics Genetics, Post Graduate Institute of Medical Education and Research |
| NM_001384732.1(CPLANE1):c.81G>A (p.Lys27=) | Single nucleotide variant | Chr5:37247618 | Uncertain significance | Synonymous variant | rs1264949337 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_001382391.1(CSPP1):c.1698-1G>C | Single nucleotide variant | Chr8:67131950 | Pathogenic | Splice acceptor variant | rs2129554176 |
.Pediatrics Genetics, Post Graduate Institute of Medical Education and Research |
| NM_173348.2(FAM149B1):c.2T>G (p.Met1Arg) | Single nucleotide variant | Chr10:73168341 | Uncertain significance | Missense variant|initiator_codon_variant | rs569932117 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_019892.6(INPP5E):c.1303C>T (p.Arg435Trp) | Single nucleotide variant | Chr9:136432563 | Pathogenic | Missense variant | rs756789619 |
.Manipal Hospitals, Manipal Hospital |
| NM_017777.4(MKS1):c.958G>A (p.Val320Ile) | Single nucleotide variant | Chr17:58210980 | Conflicting classifications of pathogenicity | Missense variant | rs386834053 |
.Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS |
| NM_017777.4(MKS1):c.1450_1453dup (p.Thr485fs) | Duplication | Chr17:58206501 - 58206502 | Pathogenic/Likely pathogenic | Frameshift variant|intron variant | rs386834044 |
.Pediatrics Genetics, Post Graduate Institute of Medical Education and Research |
| NM_016464.5(TMEM138):c.287A>G (p.His96Arg) | Single nucleotide variant | Chr11:61366203 | Pathogenic/Likely pathogenic | Missense variant|non-coding transcript variant | rs387907132 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_001173990.3(TMEM216):c.218G>A (p.Arg73His) | Single nucleotide variant | Chr11:61393965 | Pathogenic/Likely pathogenic | Missense variant | rs201108965 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001077418.3(TMEM231):c.241C>T (p.Leu81Phe) | Single nucleotide variant | Chr16:75555872 | Conflicting classifications of pathogenicity | Missense variant|non-coding transcript variant | rs376555896 |
.Lifecell International Pvt. Ltd |
| NM_153704.6(TMEM67):c.514C>T (p.Arg172Ter) | Single nucleotide variant | Chr8:93765413 | Pathogenic/Likely pathogenic | Nonsense|non-coding transcript variant | rs765468645 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_153704.6(TMEM67):c.2086C>T (p.Leu696Phe) | Single nucleotide variant | Chr8:93797456 | Conflicting classifications of pathogenicity | Missense variant|non-coding transcript variant | rs863225238 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
Indian Institutes & Variant Submission Overview
Chromosome-wise Variant Distribution