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LOVD - Variant listings for COL1A1

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+/+ 01_52 GRCh37 chr17:g.47332514_49565743del - - Deletion Whole gene deletion - - - - COL1A1_00905 Family 1 OI I Bardai et al., 2016 DNA array CGH, CNGP, PCR, SEQ The deletion in this patient spans 47 genes including COL1A1. -
+/+ 01-06 c.(?_-119)_(543+33_544-42)del - - Deletion Multi-exon deletion p.? - - - COL1A1_00992 AN_004006 OI IV Italy:Bologna DNA MLPA The patient harbours a deletion of exons 1 to 6. The 5´ break-point lies somewhere 5´ to the start of transcription. The 3´ break-point lies somewhere within intron 6 between the +33 and -42 positions. -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000791 OI I United Kingdom (Great Britain):Sheffield DNA MLPA - -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000461 OI I van Dijk et al., 2010, Pals, Netherlands: Amsterdam DNA MLPA This is patient I.1 in family 4 in van Dijk et al., 2010 -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000460 OI I van Dijk et al., 2010, Pals, Netherlands: Amsterdam DNA MLPA This is patient I.2 in family 2 in van Dijk et al., 2010 -
+/? 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000462 OI I Pals, Netherlands: Amsterdam DNA MLPA Amsterdam patient ID: VU3 -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000467 OI I van Dijk et al., 2010, Pals, Netherlands: Amsterdam DNA MLPA This is patient I.2 in family 3 in van Dijk et al., 2010 -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 AN_000464 OI I van Dijk et al., 2010, Pals, Netherlands: Amsterdam DNA MLPA This patient II.1 in family 1 in van Dijk et al., 2010 -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_00617 Case 24-2014 OI I Mannstadt et al., 2014 DNA aCGH The patient has a 1.035 Mb deletion encompassing at least 28 genes including COL1A1. -
+/+ 01_52 c.(?_-126)_(*1406_?)del - - Deletion Whole gene deletion - - - - COL1A1_01298 P39 OI IV Liu et al., 2017 DNA SEQ - Chinese
+/+ 01_52 chr17q21.33_q23.1del - - Deletion Whole gene deletion - - - - COL1A1_00366 816 OI I Pollitt et al., 2006 DNA FISH This patient also had micrognathia and cleft palate (Robin sequence), marfanoid features, blue sclerae and had a fracture at birth with osteopaenia on X-rays. The deletion was demonstrated by FISH analysis, but the identities of the non-hybridising probes are not given. -
+/+ 01_52 GRCh37 chr17:g.47554863_49471989del - - Deletion Whole gene deletion - - - - COL1A1_00903 DECIPHER 255632 - DECIPHER DNA Unknown The deletion in this patient spans 46 genes including COL1A1. The patient phenotype is described as "Abnormality of the esophagus", "Abnormality of the face" and "Intellectual disability". -
+/+ 01_52 GRCh37 chr17:g.47699383_49331643del - - Deletion Whole gene deletion - - - - COL1A1_00904 DECIPHER 267067 - DECIPHER DNA Unknown The deletion in this patient spans 43 genes including COL1A1. The patient phenotype is described as "Delayed speech and language development", "Joint laxity","Kyphosis" and "Osteoporosis". -
+/+ 01_52 GRCh37 chr17:g.48099388_49348322del - - Deletion Whole gene deletion - - - - COL1A1_00906 Family 2 OI I Bardai et al., 2016 DNA array CGH, CNGP, PCR, SEQ The deletion in this patient spans 34 genes including COL1A1. -
+/+ 01_52 GRCh37 chr17:g.48211636_48289249del - - Deletion Whole gene deletion - - - - COL1A1_00908 Family 4 OI I Bardai et al., 2016 DNA array CGH, CNGP, PCR, SEQ The deletion in this patient spans 4 genes including COL1A1. -
+/+ 01_52 GRCh37 chr17:g.48242601_48379926del - - Substitution Whole gene deletion - - - - COL1A1_00907 Family 3 OI I Bardai et al., 2016 DNA array CGH, CNGP, PCR, SEQ The deletion in this patient spans 4 genes including COL1A1. -
+/+ 01_52 GRCh37 chr17:g.48261783_48280296del - - Deletion Whole gene deletion - - - - COL1A1_00909 Family 5 OI I Bardai et al., 2016 DNA array CGH, CNGP, PCR, SEQ The deletion in this patient spans just COL1A1. -
+/+ 01_52 NCBI36.1 chr17:g.44909862_48312957del - - Deletion Whole gene deletion - - - - COL1A1_00910 OI Harbuz et al., 2013 DNA array CGH The patient has an unbalanced translocation involving chromosomes 7 and 17 with a deletion of 17q21.33-q22 which spans the COL1A1 gene. -
+/+ 01 c.1A>C - - Substitution Initiating methionine p.(Met?) - - - COL1A1_01316 UA32 OI I Zhytnik et al. 2019, Estonia:Tartu DNA PCR, SEQ - Ukrainian
+/+ 01 c.1A>G - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00546 AN_000804 OI I Italy:Verona DNA DHPLC, PCR, SEQ - Caucasian
+/+ 01 c.1A>G - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00546 AN_000805 OI IA Italy:Verona DNA DHPLC, PCR, SEQ - Caucasian
+/+ 01 c.2T>C - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00460 AN_000101 OI I Canada:Montreal DNA SEQ - -
+/+ 01 c.2T>C - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00460 AN_000042 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 01 c.2T>G - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00883 OI I Cho et al., 2015 DNA PCR, SEQ The protein-level consequence of the sequence variant is incorrectly reported as p.Met1Arg. Korean
+/+ 01 c.3G>T - - Substitution Initiating methionine p.(Met1?) - - - COL1A1_00631 2943 Fracturing bone disease Spain:Valencia DNA SEQ - -
?/+ 01 c.37_38insC - - Insertion Frameshift p.Leu13Serfs*37 - - - COL1A1_00943 1517 OI I Bardai et al., 2016, Canada:Montreal DNA SEQ - -
+/+ 01 c.38T>G - - Substitution Nonsense p.(Leu13*) - - - COL1A1_00823 Individual V3 OI I Rauch et al., 2014 DNA mPCR, SEQ - -
+/+ 01 c.64G>C dbSNP - Substitution Missense p.(Gly22Arg) - - - COL1A1_00003 443 OI II Pollitt et al., 2006 DNA SEQ - -
+/+ 01 c.64G>C dbSNP - Substitution Missense p.(Gly22Arg) - - - COL1A1_00003 AN_000079 OI II Italy:Bologna DNA DHPLC, SEQ - -
+/+ 01 c.65_70del - - Deletion In-frame deletion p.(Gly22_Gln23del) - - - COL1A1_00868 AN_005049 OI III Lindahl et al., 2015, Sweden:Uppsala DNA PCR, SEQ - Swedish
+/+ 01 c.67C>T - - Substitution Nonsense p.Q23* - - - COL1A1_01182 P1 OI I Liu et al., 2017 DNA SEQ - Chinese
?/+? 01 c.77G>A - - Substitution Missense p.(Gly26Asp) - - - COL1A1_00579 AN_000701 OI United Kingdom (Great Britain):Sheffield DNA SEQ - -
+/+ 01 c.77G>A
    + c.2461G>A
- - Substitution Missense p.(Gly26Asp) - - - COL1A1_00579 Patient 1 OI VIII Fuccio et al., 2011 DNA DGGE, PCR, SEQ This patient is reported to harbour two COL1A1 variants, either of which would be expected to result alone in producing the OI phenotype. The c.77G>A variant is previously reported as causing OI I and the frequent c.2461G>A variant causes predominantly OI types III and IV. The possible parental origin of these variants is not reported and the matter of the patient having two disease-causing variants is not discussed by the authors. Although the OI type is not recorded in the publication, the authors have provided this information subsequently. -
+/+ 01 c.79C>T - - Substitution Nonsense p.(Gln27*) - - - COL1A1_00549 AN_000808 OI I Italy:Verona DNA DHPLC, PCR, SEQ - Caucasian
+/+ 01 c.81delA - - Deletion Frameshift p.(Val28Serfs*46) - - - COL1A1_00922 Pateint 4 OI Balasubramanian et al., 2016 DNA SEQ - Canadian
+/+ 01 c.91C>T dbSNP ClinVar Substitution Nonsense p.(Gln31*) - - - COL1A1_01071 OI0005 OI I United Kingdom (Great Britain):Cambridge DNA SEQ - -
+/+ 01i c.103+1G>A dbSNP - Substitution Splice site - - - - COL1A1_00368 Patient 27 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 01i c.103+1G>A dbSNP - Substitution Splice site - - - - COL1A1_00368 AN_004007 OI I Italy:Bologna DNA HRM, SEQ - -
+/+ 01i c.103+2T>C - - Substitution Splice site - - - - COL1A1_01054 VN18 OI IV Ho Duy et al., 2016 DNA PCR, SEQ - Vietnamese
+/+ 01i c.103+2T>C - - Substitution Splice site - - - - COL1A1_01054 VN99 OI I Ho Duy et al., 2016 DNA PCR, SEQ - Vietnamese
+/+ 1i c.104-441G>T
    + c.2235+1G>A
- - Substitution Other - - - - COL1A1_01234 OI III Jaleč et al., 2019 DNA CGP The patient's sequence variant is not reported in the published account but was supplied to the database by the authors. The c.2235+1G>A splice site variant is the primary cause of the OI phenotype. The c.104-441G>T variant lies in within the binding site of the transcription factor SP1 and can be considered as a functional SNP that results in reduced BMD. -
?/+? 01i c.104-13_104-12delinsAA - - Insertion/Deletion Cryptic splice site - - - - COL1A1_00937 Patient #12 - Zarate et al., 2016 DNA PCR, SEQ The variant, incorrectly reported as c.104-13_-12CC>AA, is predicted to create a new 3´ splice site resulting in a shifted reading frame. The authors describe the variant as a VUS. -
+/+ 01i c.104-3C>G dbSNP - Substitution Splice site - - - - COL1A1_00142 Patient 24 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 01i c.104-1G>A - - Substitution Splice site - - - - COL1A1_00886 Sample 1 OI Wang et al., 2015 Wang et al., 2015 DNA PCR, SEQ, SeqArray - Chinese
+/+ 01i c.104-1G>C - - Substitution Splice site - - - - COL1A1_00850 OI I Zhang et al., 2014 DNA PCR, SEQ - Chinese
+/+ 01i-38i c.104-?_2613+?del - - Deletion Multi-exon deletion - - - - COL1A1_00753 AN_000465 OI I Pals, Netherlands: Amsterdam DNA MLPA - -
+/+ 02 c.111_117del - - Deletion Frameshift p.(Ile38Alafs*34) - - - COL1A1_00873 AN_004956 OI IA Lindahl et al., 2015, Sweden:Uppsala DNA PCR, SEQ - Swedish
+/+ 02 c.120C>A - - Substitution Nonsense p.Cys40* - - - COL1A1_00993 AN_004008 OI I Italy:Bologna DNA HRM, SEQ - -
+/+ 02 c.120C>A - - Substitution Nonsense p.Cys40* - - - COL1A1_00993 AN_004009 OI I Italy:Bologna DNA HRM, SEQ - -
+/+ 02 c.141C>A - - Substitution Nonsense p.(Tyr47*) - - - COL1A1_00932 OI17 OI IA Hruskova et al., 2016 DNA PCR, SEQ - Czech
+/+ 02 c.143dupA - - Duplication Frameshift p.(His48Glnfs*2) - - - COL1A1_01183 P2 OI I Liu et al., 2017 DNA SEQ - Chinese
+/+ 02 c.148C>T - - Substitution Nonsense p.(Arg50*) - - - COL1A1_01095 P3 OI I Liu et al., 2017 DNA SEQ - Chinese
+/+ 02 c.158G>A - - Substitution Nonsense p.Trp53* - - - COL1A1_00994 AN_004010 OI IV Italy:Bologna DNA HRM, SEQ - -
+/+ 02 c.158G>A - - Substitution Nonsense p.Trp53* - - - COL1A1_00994 AN_004011 OI IV Italy:Bologna DNA HRM, SEQ - -
+/+ 02 c.174C>A - - Substitution Nonsense - - p.(Cys58*) - COL1A1_00920 OI_14/02 OI Turkey:Edirne DNA HTS - Turkish
-/- 02 c.177G>T dbSNP - Substitution Silent p.(=) - - - COL1A1_00500 - Mackay et al., 1993 Chan et al., 2008 Bodian et al., 2009 DNA PCR, SEQ - -
+/+ 02 c.182G>T - - Substitution Missense p.(Cys61Phe) - - - COL1A1_00686 C1 OI I Zhang et al., 2011 DNA PCR, SEQ - Han Chinese
+/+ 02 c.182G>T - - Substitution Missense p.(Cys61Phe) - - - COL1A1_00686 OI23 OI III Hruskova et al., 2016 DNA PCR, SEQ - Czech
+/+ 02 c.189C>A - - Substitution Nonsense p.Cys63* - - - COL1A1_00925 OI United States:Houston DNA PCR, SEQ - -
+/+ 02 c.189C>A - - Substitution Nonsense p.Cys63* - - - COL1A1_00925 Patient 4 OI - DNA CNGP, PCR, SEQ The variant in this patient would be consistent with OI type I. Caucasian
+/+ 02 c.198_204dup - - Duplication Frameshift p.(Leu69Glnfs*6) - - - COL1A1_00931 MOOI-I 4 OI I Kaneto et al., 2014 DNA PCR, SEQ - -
+/+ 02 c.199A>T - - Substitution Nonsense p.(Lys67*) - - - COL1A1_00536 AN_000023 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 02 c.231delG - - Deletion Frameshift p.(Thr78Profs*76) - - - COL1A1_01164 91 OI I Augusciak-Duma et al., 2018 DNA SEQ - Polish
+/+ 02 c.246delC dbSNP - Deletion Frameshift p.(Gly83Alafs*182) - - - COL1A1_00285 Patient 38 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ This mutation is incorrectly described as c.243delC in Hartikka et al., 2004. -
+/+ 02 c.253G>T - - Substitution Nonsense p.(Glu85*) - - - COL1A1_01175 P27 OI Mrosk et al., 2018 DNA SEQ The patient was heterozygous, while the mutation was absent in the patient's parents. Indian
-?/-? 02 c.266G>T
    + COL1A2 (1)
- - Substitution Missense p.(Gly89Val) - - - COL1A1_00629 AN_000922 OI III/IV United Kingdom (Great Britain):Sheffield DNA SEQ - -
+/+ 02 c.266_266delGinsCGCCGTCCCGGGGA - - Insertion/Deletion Frameshift p.(Gly89Alafs*84) - - - COL1A1_00578 AN_000166 OI I Canada:Montreal DNA SEQ - Caucasian
+/+ 02 c.268_299-60del - - Deletion Other - - - - COL1A1_00687 C2 OI I Zhang et al., 2011 DNA PCR, SEQ The deletion spans from exon 2 to intron 2 and probably results in loss of exon 2, resulting in a frameshift. Han Chinese
+/+ 02 c.281T>A - - Substitution Nonsense p.(Val94Asp) - - - COL1A1_01063 OI IV Yang et al., 2018 DNA PCR, SEQ - Han Chinese
+/+ 02 c.285C>A - - Substitution Nonsense p.(Cys95*) - - - COL1A1_00632 4006 OI I Spain:Valencia DNA SEQ - Caucasian
+/+ 02i c.299-5_313del - - Deletion Splice site - - - - COL1A1_00585 AN_000703 OI I United Kingdom (Great Britain):Sheffield DNA SEQ - -
+/+ 02i c.299-2A>G - - Substitution Splice site - - - - COL1A1_01184 P4 OI IV Liu et al., 2017 DNA SEQ - Chinese
+/+ 02i c.299-1G>C - - Substitution Splice site - - - - COL1A1_00552 AN_000030 OI I Italy:Bologna DNA DHPLC, SEQ - -
+?/+ 02i c.299-1G>C
    + c.1984-5C>A
- - Substitution Splice site - - - - COL1A1_00552 AN_000702 OI I United Kingdom (Great Britain):Sheffield DNA SEQ No family studies done. -
+/+ 02i c.299-1G>C - - Substitution Splice site - - - - COL1A1_00552 AN_004012 OI I Italy:Bologna DNA SEQ - -
+/+ 02i c.299-1G>C - - Substitution Splice site - - - - COL1A1_01235 EE19 OI IV Zhytnik et al., 2017, Estonia:Tartu DNA SEQ - Estonian
+/+ 02 c.299_300del - - Deletion Frameshift p.(Glu100Valfs*68) - - - COL1A1_00995 AN_004013 OI I Italy:Bologna DNA HRM, SEQ - -
+/+ 02 c.299_300insC dbSNP - Insertion Frameshift p.(Glu100Aspfs*69) - - - COL1A1_00286 Patient 42 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 02 c.299_300insC dbSNP - Insertion Frameshift p.(Glu100Aspfs*69) - - - COL1A1_00286 Patient 45 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 03 c.314_324del - - Deletion Frameshift p.(Gln105Argfs*60) - - - COL1A1_00688 C3 OI I Zhang et al., 2011 DNA PCR, SEQ - Han Chinese
+/+ 03 c.333_333+1delinsTC - - Insertion/Deletion Splice site - - - - COL1A1_00143 Patient 49 OI I Ries-Levavi et al., 2004, United States:Seattle DNA DGGE, PCR, SEQ This mutation was also found in an additional family member (patient 50). -
+/+ 03i c.333+2T>C dbSNP - Substitution Splice site - - - - COL1A1_00169 Patient 31 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 03i c.333+2T>C dbSNP - Substitution Splice site - - - - COL1A1_00169 AN_004949 OI IA Lindahl et al., 2015, Sweden:Uppsala DNA PCR, SEQ - Swedish
+/+ 03i c.333+2T>C dbSNP - Substitution Splice site - - - - COL1A1_00169 AN_005068 OI IA Lindahl et al., 2015, Sweden:Uppsala DNA PCR, SEQ - Swedish
+/+ 03i c.334-9A>G - - Substitution Splice site - - - - COL1A1_00911 Family F1 OI I Lin et al., 2015 DNA PCR, SEQ The variant in this patient is incorrectly reported as c.333-9A>G. Taiwanese
+/+ 03i c.334-2A>G dbSNP - Substitution Splice site - - - - COL1A1_00201 Patient 32 OI I Hartikka et al., 2004 DNA CSGE, PCR, SEQ - -
+/+ 04 c.358C>T - - Substitution Nonsense p.Arg120* - - - COL1A1_00944 959.1 OI I Bardai et al., 2016, Canada:Montreal DNA CNGP - -
+/+ 04i c.370-3_370-1delinsTC - - Insertion/Deletion Splice site - - - - COL1A1_00996 AN_004014 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 04i c.370-3_370-1delinsTC - - Insertion/Deletion Splice site - - - - COL1A1_00996 AN_004015 OI I Italy:Bologna DNA SEQ - -
+/+ 04i c.370-1G>A - - Substitution Splice site - - - - COL1A1_00689 C4 OI I Zhang et al., 2011 DNA PCR, SEQ - Han Chinese
+/+ 05 c.386delC dbSNP - Deletion Frameshift p.(Pro129Leufs*136) - - - COL1A1_00288 OI IV Pollitt et al., 2006 DNA PCR, SEQ - -
+/+ 05 c.386delC dbSNP - Deletion Frameshift p.(Pro129Leufs*136) - - - COL1A1_00288 2943 OI I Spain:Valencia DNA SEQ - Caucasian
+/+ 05 c.386delC dbSNP - Deletion Frameshift p.(Pro129Leufs*136) - - - COL1A1_00288 AN_000054 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 05 c.386delC dbSNP - Deletion Frameshift p.(Pro129Leufs*136) - - - COL1A1_00288 AN_004016 OI I Italy:Bologna DNA HRM, SEQ - -
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 OI I Pollitt et al., 2006 DNA PCR, SEQ This mutation was incorrectly described in terms of the HGVS nomenclature in Pollitt et al., 2006. -
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 AN_000005 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 AN_000008 OI I Italy:Bologna DNA DHPLC, SEQ - -
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 AN_000704 OI I United Kingdom (Great Britain):Sheffield DNA SEQ - -
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 Family F3 OI I Lin et al., 2015 DNA PCR, SEQ The variant in this patient is incorrectly described as c.386_387insC. Taiwanese
+/+ 05 c.386dupC - - Duplication Frameshift p.(Gly130Trpfs*39) - - - COL1A1_00287 AN_004017 OI I Italy:Bologna DNA DHPLC, SEQ - -
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Legend: [ COL1A1 full legend ]
Sequence variations are described basically as recommended by the Ad-Hoc Committee for Mutation Nomenclature (AHCMN), with the recently suggested additions (den Dunnen JT and Antonarakis SE [2000], Hum.Mut. 15:7-12); for a summary see Nomenclature. Genomic Reference Sequence.
Path.: Variant pathogenicity, in the format Reported/Concluded; '+' indicating the variant is pathogenic, '+?' probably pathogenic, '-' no known pathogenicity, '-?' probably no pathogenicity, '?' effect unknown. Exon: Exon numbering. DNA change: Variation at DNA-level. If present, "Full Details" will show you the the full-length entry. dbSNP: dbSNP ClinVar: ClinVar Type: Type of variant at DNA level. Mutation effect: Mutation effect at protein or RNA level. Protein: Variation at protein level. Legacy change: "Traditional" (legacy) amino acid numbering RNA change: Variation at RNA-level, (?) unknown but probably identical to DNA. Re-site: Variant creates (+) or destroys (-) a restriction enzyme recognition site. COL1A1 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided. Patient ID: Internal reference to the patient. Disease: Disease phenotype, as reported in paper/by submitter, unless modified by the curator. Reference: Reference describing the variation, "Submitted:" indicating that the mutation was submitted directly to this database. Template: Variant detected in DNA, RNA and/or Protein. Technique: Technique used to detect the variation. Ethnic origin: Ethnic origin of patient