An
Autosomal dominant, Autosomal recessive, X-linked dominant
mode(s) within the
Bone disorders
category
Benign/Likely benign
1
Conflicting classifications of pathogenicity
4
Likely pathogenic
15
Pathogenic
18
Pathogenic/Likely pathogenic
10
Uncertain significance
10
| Variant name | Variant type | GRCH38 location | Germline classification | Molecular consequence | dbSNP_ID | Submitter |
|---|---|---|---|---|---|---|
| NM_006129.5(BMP1):c.1215C>G (p.Ile405Met) | Single nucleotide variant | Chr8:22194092 | Uncertain significance | Missense variant|non-coding transcript variant | rs1586459952 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_006129.5(BMP1):c.916A>C (p.Ser306Arg) | Single nucleotide variant | Chr8:22179784 | Uncertain significance | Missense variant|non-coding transcript variant | rs1357950133 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_001854.4(COL11A1):c.3619G>A (p.Gly1207Ser) | Single nucleotide variant | Chr1:102923371 | Uncertain significance | Missense variant|non-coding transcript variant | rs1234981157 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000088.4(COL1A1):c.1663C>A (p.Pro555Thr) | Single nucleotide variant | Chr17:50194135 | Likely pathogenic | Missense variant |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
|
| NM_000088.4(COL1A1):c.4342G>C (p.Gly1448Arg) | Single nucleotide variant | Chr17:50185555 | Likely pathogenic | Missense variant | rs2509152842 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.3653C>T (p.Ala1218Val) | Single nucleotide variant | Chr17:50186801 | Pathogenic/Likely pathogenic | Missense variant | rs201398339 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.2831delG | Deletion | Chr17:50189274 | Pathogenic | Splice acceptor variant | rs2144549369 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.2579G>A (p.Gly860Glu) | Single nucleotide variant | Chr17:50189893 | Likely pathogenic | Missense variant | rs72653142 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.3871T>G (p.Cys1291Gly) | Single nucleotide variant | Chr17:50186451 | Likely pathogenic | Missense variant | rs2144534929 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.4189G>T (p.Glu1397Ter) | Single nucleotide variant | Chr17:50185837 | Pathogenic | Nonsense | rs902407269 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.2056G>A (p.Gly686Ser) | Single nucleotide variant | Chr17:50191859 | Likely pathogenic | Missense variant | rs1404470949 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.4166T>C (p.Leu1389Pro) | Single nucleotide variant | Chr17:50185860 | Likely pathogenic | Missense variant | rs2144531821 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.2029-1G>T | Single nucleotide variant | Chr17:50191887 | Pathogenic | Splice acceptor variant | rs1201602830 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.3281G>C (p.Gly1094Ala) | Single nucleotide variant | Chr17:50187964 | Likely pathogenic | Missense variant | rs2144542715 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.1155+1G>C | Single nucleotide variant | Chr17:50195566 | Pathogenic/Likely pathogenic | Splice donor variant | rs72648315 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.1094G>T (p.Gly365Val) | Single nucleotide variant | Chr17:50195628 | Pathogenic/Likely pathogenic | Missense variant | rs66494876 |
.Division of Medical Genetics, Department of Pediatrics, All India Institute of Medical Sciences, New Delhi |
| NM_000088.4(COL1A1):c.2110G>A (p.Gly704Ser) | Single nucleotide variant | Chr17:50191805 | Pathogenic | Missense variant | rs67368147 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000088.4(COL1A1):c.578dup (p.Gly194fs) | Duplication | Chr17:50198170 - 50198171 | Pathogenic/Likely pathogenic | Frameshift variant | rs1598300304 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000088.4(COL1A1):c.3055G>T (p.Gly1019Cys) | Single nucleotide variant | Chr17:50188786 | Pathogenic | Missense variant | rs1598288342 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000088.4(COL1A1):c.2172del (p.Gly725fs) | Deletion | Chr17:50191446 | Pathogenic | Frameshift variant | rs1567757138 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_000088.4(COL1A1):c.769G>A (p.Gly257Arg) | Single nucleotide variant | Chr17:50197045 | Pathogenic | Missense variant | rs72645321 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000088.4(COL1A1):c.3141TCCTGGTGC[1] (p.1047APG[2]) | Microsatellite | Chr17:50188579 - 50188587 | Pathogenic | Inframe_deletion | rs74315111 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000089.4(COL1A2):c.825_842dup (p.Pro281_Arg282insAlaGlyProAlaGlyPro) | Duplication | Chr7:94409348 - 94409349 | Uncertain significance | Inframe_insertion |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
|
| NM_000089.4(COL1A2):c.821G>T (p.Gly274Val) | Single nucleotide variant | Chr7:94409350 | Pathogenic | Missense variant | rs67675951 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000089.4(COL1A2):c.1631G>C (p.Gly544Ala) | Single nucleotide variant | Chr7:94413913 | Likely pathogenic | Missense variant | rs72658135 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000089.4(COL1A2):c.2711G>A (p.Gly904Glu) | Single nucleotide variant | Chr7:94425154 | Likely pathogenic | Missense variant | rs775246283 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000089.4(COL1A2):c.279+3A>C | Single nucleotide variant | Chr7:94401623 | Likely pathogenic | Intron variant | rs762201938 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000089.4(COL1A2):c.231del (p.Phe77fs) | Deletion | Chr7:94401570 | Pathogenic | Frameshift variant | rs2115865220 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000089.4(COL1A2):c.1630G>T (p.Gly544Cys) | Single nucleotide variant | Chr7:94413912 | Likely pathogenic | Missense variant | rs72658134 |
.Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital |
| NM_000089.4(COL1A2):c.875G>A (p.Gly292Asp) | Single nucleotide variant | Chr7:94409404 | Pathogenic/Likely pathogenic | Missense variant | rs1131692167 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_000089.4(COL1A2):c.757G>C (p.Gly253Arg) | Single nucleotide variant | Chr7:94408788 | Uncertain significance | Missense variant | rs1584318623 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000089.4(COL1A2):c.2026-1_2042dup | Duplication | Chr7:94419496 - 94419497 | Conflicting classifications of pathogenicity | Splice acceptor variant | rs1584325529 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000089.4(COL1A2):c.1613G>A (p.Gly538Asp) | Single nucleotide variant | Chr7:94413895 | Conflicting classifications of pathogenicity | Missense variant | rs1584322496 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000393.5(COL5A2):c.4174C>A (p.Leu1392Ile) | Single nucleotide variant | Chr2:189035095 | Uncertain significance | Missense variant | rs748999143 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_006371.5(CRTAP):c.634C>T (p.Arg212Ter) | Single nucleotide variant | Chr3:33124420 | Pathogenic/Likely pathogenic | Nonsense | rs137853944 |
.Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS |
| NM_021939.4(FKBP10):c.1256+1G>A | Single nucleotide variant | Chr17:41820462 | Pathogenic/Likely pathogenic | Splice donor variant |
.Department Of Genetics, Lifeline Super Speciality Hospital, Adoor. |
|
| NM_021939.4(FKBP10):c.1479_1481delinsTCAG (p.Leu494fs) | Indel | Chr17:41821733 - 41821735 | Likely pathogenic | Frameshift variant |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
|
| NM_021939.4(FKBP10):c.1399+51del | Deletion | Chr17:41821112 | Benign/Likely benign | Intron variant | rs10522999 |
.Centre for Medical Genetics, Mumbai |
| NM_021939.4(FKBP10):c.918-2A>G | Single nucleotide variant | Chr17:41819528 | Likely pathogenic | Splice acceptor variant | rs1597907877 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_000158.4(GBE1):c.1843G>C (p.Ala615Pro) | Single nucleotide variant | Chr3:81535286 | Likely pathogenic | Missense variant | rs768485124 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001025295.3(IFITM5):c.119C>T (p.Ser40Leu) | Single nucleotide variant | Chr11:299372 | Pathogenic | Missense variant | rs786201032 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_001025295.3(IFITM5):c.-14C>T | Single nucleotide variant | Chr11:299504 | Pathogenic | 5 prime UTR variant | rs587776916 |
.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 |
| NM_002615.7(SERPINF1):c.194T>C (p.Leu65Pro) | Single nucleotide variant | Chr17:1769961 | Uncertain significance | Missense variant|5 prime UTR variant | rs760504051 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Suma Genomics |
| NM_002615.7(SERPINF1):c.250dup (p.Ser84fs) | Duplication | Chr17:1770016 - 1770017 | Pathogenic | Frameshift variant|5 prime UTR variant |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
|
| NM_022356.4(P3H1):c.2051_2054del (p.Glu684fs) | Microsatellite | Chr1:42747273 - 42747276 | Pathogenic | Frameshift variant | rs2124076122 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_022356.4(P3H1):c.1980dup (p.Val661fs) | Duplication | Chr1:42747346 - 42747347 | Pathogenic/Likely pathogenic | Frameshift variant | rs1570453963 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_022356.4(P3H1):c.2131dup (p.Leu711fs) | Duplication | Chr1:42746776 - 42746777 | Pathogenic/Likely pathogenic | 3 prime UTR variant|frameshift variant | rs1570452407 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_022356.4(P3H1):c.1346-1G>C | Single nucleotide variant | Chr1:42752665 | Pathogenic | Splice acceptor variant | rs886042897 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Neuberg Centre For Genomic Medicine, NCGM |
| NM_000942.5(PPIB):c.399_401dup (p.Gly134_Pro135insGly) | Duplication | Chr15:64156851 - 64156852 | Uncertain significance | Inframe_indel|inframe_insertion|3 prime UTR variant|non-coding transcript variant | rs886039912 |
.Diagnostics Division, CENTRE FOR DNA FINGERPRINTING AND DIAGNOSTICS |
| NM_002615.7(SERPINF1):c.532C>T (p.Gln178Ter) | Single nucleotide variant | Chr17:1771964 | Pathogenic | Nonsense|5 prime UTR variant | rs2543482778 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_002615.7(SERPINF1):c.-37C>A | Single nucleotide variant | Chr17:1762085 | Uncertain significance | 5 prime UTR variant | rs1039127862 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India |
| NM_002615.7(SERPINF1):c.826TTC[1] (p.Phe277del) | Microsatellite | Chr17:1776569 - 1776571 | Conflicting classifications of pathogenicity | Inframe_deletion | rs773952734 |
.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 |
| NM_002615.7(SERPINF1):c.77dup (p.Glu27fs) | Duplication | Chr17:1766981 - 1766982 | Pathogenic | Frameshift variant|intron variant | rs1272920425 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_002615.7(SERPINF1):c.907C>T (p.Arg303Ter) | Single nucleotide variant | Chr17:1776652 | Pathogenic/Likely pathogenic | Nonsense | rs763291398 |
.GenePathDx, GenePath diagnostics |
| NM_001235.5(SERPINH1):c.1214G>A (p.Arg405His) | Single nucleotide variant | Chr11:75572040 | Uncertain significance | Missense variant | rs781125078 |
.Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics |
| NM_005430.4(WNT1):c.506dup (p.Cys170fs) | Duplication | Chr12:48980564 - 48980565 | Pathogenic | Frameshift variant | rs779969402 |
.Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India .Neuberg Centre For Genomic Medicine, NCGM |
| NM_005430.4(WNT1):c.501G>C (p.Trp167Cys) | Single nucleotide variant | Chr12:48980566 | Conflicting classifications of pathogenicity | Missense variant | rs1592257435 |
.Paediatric Orthopaedics Research Lab, Christian Medical College |
| NM_005430.4(WNT1):c.104+4_104+44del | Deletion | Chr12:48978757 - 48978797 | Likely pathogenic | Intron variant | rs1555178899 |
.Department of Paediatric Medicine, Post Graduation Institute of Medical Education and Research |
Indian Institutes & Variant Submission Overview
Chromosome-wise Variant Distribution