Neuronal ceroid lipofuscinosis
An Autosomal dominant, Autosomal recessive mode(s) within the Metabolic disorders/Lysosomal storage disorders category
Benign/Likely benign
1
Conflicting classifications of pathogenicity
7
Likely pathogenic
16
Pathogenic
13
Pathogenic/Likely pathogenic
3
Uncertain significance
3
| Variant name | Variant type | GRCH38 location | Germline classification | Molecular consequence | dbSNP_ID | Submitter |
|---|---|---|---|---|---|---|
| Single allele | Duplication | Chr16:28482106 - 28486650 | Pathogenic |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
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| NM_001042432.2(CLN3):c.838-3C>G | Single nucleotide variant | Chr16:28482548 | Likely pathogenic | Intron variant | rs1437110742 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_006493.4(CLN5):c.570del (p.Asn190fs) | Deletion | Chr13:77000462 | Likely pathogenic | 3 prime UTR variant|frameshift variant |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
|
| NM_006493.4(CLN5):c.361G>A (p.Gly121Arg) | Single nucleotide variant | Chr13:76995923 | Likely pathogenic | Missense variant | rs1309552809 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_006493.4(CLN5):c.525G>A (p.Trp175Ter) | Single nucleotide variant | Chr13:76996087 | Likely pathogenic | Nonsense | rs2501140694 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_006493.4(CLN5):c.626A>G (p.Tyr209Cys) | Single nucleotide variant | Chr13:77000518 | Likely pathogenic | 3 prime UTR variant|missense variant | rs762787810 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_006493.4(CLN5):c.350A>C (p.His117Pro) | Single nucleotide variant | Chr13:76995912 | Likely pathogenic | Missense variant | rs2501139368 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_017882.3(CLN6):c.775G>A (p.Gly259Ser) | Single nucleotide variant | Chr15:68208301 | Conflicting classifications of pathogenicity | Missense variant | rs150363441 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics .Neuberg Centre For Genomic Medicine, NCGM |
| NM_017882.3(CLN6):c.185G>A (p.Arg62His) | Single nucleotide variant | Chr15:68218549 | Conflicting classifications of pathogenicity | Missense variant | rs751486476 |
.Child Neurology Division, Pediatrics Department, KAHER's Jawaharlal Nehru Medical College, Belagavi .Lifecell International Pvt. Ltd |
| NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del) | Microsatellite | Chr15:68208280 - 68208282 | Conflicting classifications of pathogenicity | Inframe_deletion | rs768422260 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_018941.4(CLN8):c.607T>C (p.Cys203Arg) | Single nucleotide variant | Chr8:1780313 | Likely pathogenic | Missense variant | rs2486488805 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_018941.4(CLN8):c.424dup (p.Ala142fs) | Duplication | Chr8:1771477 - 1771478 | Pathogenic | Frameshift variant | rs2486442031 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_018941.4(CLN8):c.447C>A (p.Cys149Ter) | Single nucleotide variant | Chr8:1771501 | Pathogenic | Nonsense | rs758707781 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_018941.4(CLN8):c.544-1G>T | Single nucleotide variant | Chr8:1780249 | Likely pathogenic | Splice acceptor variant | rs2486488212 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_153033.5(KCTD7):c.280C>T (p.Arg94Trp) | Single nucleotide variant | Chr7:66633410 | Conflicting classifications of pathogenicity | Missense variant | rs387907260 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000243.3(MEFV):c.726C>A (p.Ser242Arg) | Single nucleotide variant | Chr16:3254342 | Pathogenic/Likely pathogenic | Missense variant|intron variant | rs104895127 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001371596.2(MFSD8):c.979del (p.Val327fs) | Deletion | Chr4:127930702 | Pathogenic | Frameshift variant | rs2546083094 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_001371596.2(MFSD8):c.699-1G>A | Single nucleotide variant | Chr4:127938839 | Pathogenic | Intron variant|splice acceptor variant | rs1739594685 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001371596.2(MFSD8):c.268G>C (p.Ala90Pro) | Single nucleotide variant | Chr4:127943923 | Uncertain significance | Missense variant | rs1553950970 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_001371596.2(MFSD8):c.935T>C (p.Ile312Thr) | Single nucleotide variant | Chr4:127930746 | Conflicting classifications of pathogenicity | Missense variant | rs556875684 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_001371596.2(MFSD8):c.894T>G (p.Tyr298Ter) | Single nucleotide variant | Chr4:127930787 | Pathogenic | Nonsense | rs118203977 | |
| NM_000310.4(PPT1):c.335T>C (p.Met112Thr) | Single nucleotide variant | Chr1:40092072 | Likely pathogenic | Missense variant|intron variant | rs2523687692 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_000310.4(PPT1):c.428A>G (p.His143Arg) | Single nucleotide variant | Chr1:40091334 | Uncertain significance | Missense variant|intron variant | rs1307096849 |
.Pediatrics Genetics, Post Graduate Institute of Medical Education and Research |
| NM_000310.4(PPT1):c.234+2T>G | Single nucleotide variant | Chr1:40092396 | Likely pathogenic | Intron variant|splice donor variant | rs2523689662 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_000310.4(PPT1):c.532del (p.Glu178fs) | Deletion | Chr1:40089414 | Pathogenic | Frameshift variant | rs878853325 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000310.4(PPT1):c.707T>A (p.Val236Glu) | Single nucleotide variant | Chr1:40078579 | Likely pathogenic | Missense variant | rs878853324 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000310.4(PPT1):c.713C>T (p.Pro238Leu) | Single nucleotide variant | Chr1:40078573 | Pathogenic/Likely pathogenic | Missense variant | rs878853322 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics .Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Lifecell International Pvt. Ltd .Suma Genomics |
| NM_000391.4(TPP1):c.1450dup (p.Ile484fs) | Duplication | Chr11:6614966 - 6614967 | Pathogenic | Frameshift variant | rs2493795977 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_000391.4(TPP1):c.182_184delinsC (p.Leu61fs) | Indel | Chr11:6618821 - 6618823 | Pathogenic | Frameshift variant | rs2493801988 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_000391.4(TPP1):c.1266_1266+1delinsTACAAACAAACA | Indel | Chr11:6615441 - 6615442 | Pathogenic | Splice donor variant | rs2493796806 |
.Human Genome Lab, NIMHANS, National Institute of Mental Health and Neuro Sciences |
| NM_000391.4(TPP1):c.688-1G>T | Single nucleotide variant | Chr11:6616860 | Pathogenic | Splice acceptor variant | rs1855593862 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000391.4(TPP1):c.1340G>C (p.Arg447Pro) | Single nucleotide variant | Chr11:6615256 | Likely pathogenic | Missense variant | rs119455956 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000391.4(TPP1):c.1080C>A (p.Asp360Glu) | Single nucleotide variant | Chr11:6616070 | Uncertain significance | Missense variant | rs1564854760 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000391.4(TPP1):c.380+5G>A | Single nucleotide variant | Chr11:6617621 | Pathogenic/Likely pathogenic | Intron variant | rs1564855725 |
.Department Of Genetics, Lifeline Super Speciality Hospital, Adoor. .Suma Genomics |
| NM_000391.4(TPP1):c.184del (p.Ser62fs) | Deletion | Chr11:6618821 | Likely pathogenic | Frameshift variant | rs1554902217 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000391.4(TPP1):c.689del (p.Phe230fs) | Deletion | Chr11:6616858 | Likely pathogenic | Frameshift variant | rs1554901898 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000391.4(TPP1):c.1435C>G (p.Pro479Ala) | Single nucleotide variant | Chr11:6614982 | Conflicting classifications of pathogenicity | Missense variant | rs756530648 | |
| NM_000391.4(TPP1):c.456G>C (p.Arg152Ser) | Single nucleotide variant | Chr11:6617353 | Likely pathogenic | Missense variant | rs869025274 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000391.4(TPP1):c.1376A>C (p.Tyr459Ser) | Single nucleotide variant | Chr11:6615220 | Likely pathogenic | Missense variant | rs864309505 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics .Neuberg Centre For Genomic Medicine, NCGM |
| NM_000391.4(TPP1):c.379C>T (p.Arg127Ter) | Single nucleotide variant | Chr11:6617627 | Pathogenic | Nonsense | rs756564767 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Neuberg Centre For Genomic Medicine, NCGM |
| NM_000391.4(TPP1):c.1016G>A (p.Arg339Gln) | Single nucleotide variant | Chr11:6616374 | Conflicting classifications of pathogenicity | Missense variant | rs765380155 |
.Human Genetics Research Lab, Central University of Jammu |
| NM_000391.4(TPP1):c.381-10dup | Duplication | Chr11:6617437 - 6617438 | Benign/Likely benign | Intron variant | rs146315473 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000391.4(TPP1):c.622C>T (p.Arg208Ter) | Single nucleotide variant | Chr11:6617040 | Pathogenic | Nonsense | rs119455955 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
Indian Institutes & Variant Submission Overview
Chromosome-wise Variant Distribution