LOVD - Variant listings for COL5A2

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-/- g.4841G>A - M58529:g.805A>G Substitution Other - - - - COL5A2_00015 - - Grond-Ginsbach et al., 2002 DNA PCR, SEQ The variant was incorrectly described as an A>G substitution at position 801 of the legacy reference sequence when in fact the variant was at position 805. Caucasian
?/- 02 c.315A>C dbSNP - Substitution Silent p.(=) - - - COL5A2_00020 - - dbSNP Unknown Unknown - -
+/+ 12i c.852+1G>C - - Substitution Splice site - - - - COL5A2_00050 AN_002546 Classical EDS Italy:Brescia DNA PCR, SEQ This is a sporadic case (de novo mutation verified). Italian
+?/+ 14i c.960+1G>A - - Substitution Splice site - - - - COL5A2_00046 AN_001709 EDS I Italy:Bologna DNA hrMCA, SEQ - -
+/+ 15i c.1006-2A>G - - Substitution Splice site p.(Gly336_Pro353del) - - - COL5A2_00037 AN_001945 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA, RNA RT-PCR, SEQ mRNA analysis confirms skipping of exon 16. -
+/+ 16i c.1059+2T>A - - Substitution Splice site p.(Gly336_Pro353del) - - - COL5A2_00038 AN_001946 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA, RNA RT-PCR, SEQ mRNA analysis confirms skipping of exon 16. -
+/+ 19 c.1186G>C - - Substitution Missense p.(Gly396Arg) - - - COL5A2_00039 AN_001947 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA PCR, SEQ - -
?/- 21 c.1311G>A dbSNP - Substitution Silent p.(=) - - - COL5A2_00021 - - dbSNP Unknown Unknown - -
?/- 21 c.1378C>T dbSNP - Substitution Missense p.(Pro460Ser) - - - COL5A2_00022 - - dbSNP Unknown Unknown The information in dbSNP is muddled. Care! -
+/+ 21 c.1401G>A - - Substitution Splice site p.(Gly435_Pro467del) r.1402_1455del - - COL5A2_00041 AN_001948 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA RT-PCR, SEQ The sequence variant at the final base of exon 21 interferes with splicing: mRNA analysis shows skipping of exon 21. -
+?/-? 21i c.1402-10T>G
    + COL3A1 (1)
- - Substitution Splice site - - - - COL5A2_00053 AN_005301 Classical EDS Weerakkody et al., 2016, Imperial College London, UK DNA CNGP Classical EDS. Clear phenotype - markedly hyperextensible skin, generalised hypermobility (Beighton 8) including marked distal hypermobility, facies suggestive of Classical EDS, no critieria met for Vascular EDS. Collagen Proteins: normal pro╬▒1(III) pattern, LM: thickened elastic fibres. EM: irregular packing of collagen fibrils (no collagen rosettes). This patient has a disease-causing variant in COL3A1 but the intronic COL5A2 VUS is unlikely to disrupt splicing. This patient is also identified with ID 636. Caucasian
-/- 23 c.1535T>C
    + c.2498C>T
- - Substitution Missense p.(Val512Ala) - - - COL5A2_00007 No. 97 Cervical artery dissection Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP The mutations were originally described as a T>C substitution at position 1683 and a C>T substitution at position 2646 each in NM_000393.2 counting from the start of the sequence. The same combination of variants was also found in an unrelated control individual, implying that these variants are probably not disease causing. The c.1535T>C variant is recorded in dbSNP. -
+/+ 24i c.1617+4A>G - NM_000393.2:c.1608+4A>G Substitution Splice site - - - - COL5A2_00019 EDS22 Classical EDS Malfait et al., 2005 DNA, RNA DHPLC, PCR, RT-PCR, SEQ, CSGE, SSCP The author has confirmed that this variant was originally mistakenly described as c.1608+4T>C using NM_000393.2 as the reference sequence. This variant is mistakenly shown as being adjacent to exon 22 in Figure 3 in Malfait and De Paepe, 2005. -
?/- 27 c.1838G>C dbSNP - Substitution Missense p.(Ser613Thr) - - - COL5A2_00023 - - dbSNP Unknown Unknown - -
?/- 27 c.1868G>A dbSNP - Substitution Missense p.(Ser623Asn) - - - COL5A2_00024 - - dbSNP Unknown Unknown - -
?/- 28 c.1903G>C dbSNP - Substitution Missense p.(Ala635Pro) - - - COL5A2_00025 - - dbSNP Unknown Unknown - -
?/- 28 c.1920G>A dbSNP - Substitution Silent p.(=) - - - COL5A2_00026 - - dbSNP Unknown Unknown - -
+/+ 28i c.1924-11T>C - - Substitution Splice site - - - - COL5A2_00051 AN_002553 Classical EDS Italy:Brescia DNA PCR, SEQ This is a sporadic case (de novo mutation verified). The splice site variant is predicted, in silico, to result in the alteration of the canonical splice acceptor site adjacent to exon 29. -
+/+ 28i c.1924-2_1928del - - Deletion Splice site - - - - COL5A2_00004 EDS3 EDS I Michalickova et al., 1998 DNA, RNA DSCA, RT-PCR, SEQ, SSCP This patient is also presented as proband C-II-I by Segev et al., 2006. In both papers, the deletion is mistakenly described as being at the junction of intron 26 with exon 27 rather than at the junction of intron 28 with exon 29. -
+/+ 29 c.1933G>A - - Substitution Missense p.(Gly645Arg) - - - COL5A2_00040 AN_001949 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA PCR, SEQ This patient was previously described as mutation-negative in the study of Malfait et al., 2005. -
+/+ 29 c.1947A>G - - Substitution Exon skip p.(Gly642_Pro659del) - - - COL5A2_00042 AN_001950 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA RT-PCR, SEQ mRNA analysis demonstrates skipping of exon 29. -
+/+ 29 c.1977G>A - - Substitution Exon skip p.(Gly642_Pro659del) - - - COL5A2_00048 AN_002533 Classical EDS Ritelli et al., 2013, Italy:Brescia DNA PCR, SEQ This sporadic case presents with a severe phenotype (de novo mutation verified). The substitution at the last base of exon 29 results in the exon being skipped. Italian
+/+ 30i c.2031+1G>T - - Substitution Splice site - - - - COL5A2_00005 EDS38 EDS I Michalickova et al., 1998 DNA, RNA DSCA, RT-PCR, SEQ, SSCP - -
?/- 34 c.2263A>C dbSNP - Substitution Missense p.(Thr755Pro) - - - COL5A2_00027 - - dbSNP Unknown Unknown - -
?/- 35 c.2376A>C dbSNP - Substitution Silent p.(=) - - - COL5A2_00028 - - dbSNP Unknown Unknown - -
-/- 37 c.2498C>T
    + c.1535T>C
- - Substitution Missense p.(Pro833Leu) - - - COL5A2_00018 No. 97 Cervical artery dissection Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP The mutations were originally described as a T>C substitution at position 1683 and a C>T substitution at position 2646 each in NM_000393.2 counting from the start of the sequence. The same combination of variants was also found in an unrelated control individual, implying that these variants are probably not disease causing. The c.1535T>C variant is recorded in dbSNP. -
+/+ 37i c.2499+2T>C - - Substitution Exon skip p.(Gly816_Pro833del) - - - COL5A2_00047 AN_002534 Classical EDS Ritelli et al., 2013, Italy:Brescia DNA, RNA PCR, RT-PCR, SEQ This sporadic case presents with a severe phenotype (de novo mutation verified). Italian
+/+ 38i c.2553+2delT - NM_000393.2:c.2544+2delT Deletion Splice site - - - - COL5A2_00016 EDS2 Classical EDS Malfait et al., 2005 DNA, RNA DHPLC, PCR, RT-PCR, SEQ, CSGE, SSCP - -
?/+ 42 c.2861dupG dbSNP - Duplication Frameshift p.(Asp955Argfs*74) - - - COL5A2_00029 - - dbSNP Unknown Unknown This variant is incorrectly described as c.2858_2859insG in dbSNP and the predicted amino acid "substitution" is wrong. In addition, the frameshift predicted by this variant would be expected to be pathogenic: a null allele. The dbSNP data concerning this variant need to be treated with caution. -
?/- 42 c.2867G>C dbSNP - Substitution Missense p.(Arg956Pro) - - - COL5A2_00031 - - dbSNP Unknown Unknown The dbSNP entry is rather muddled for this variant. -
+/+ 43i c.3040-2A>G - - Substitution Splice site p.(Gly1014_Glu1049del) - - - COL5A2_00043 AN_001951 Classical EDS Belgium:Ghent DNA, RNA RT-PCR, SEQ mRNA analysis confirms skipping of exon 44. -
?/+ 44 c.3054dupA dbSNP - Duplication Frameshift p.(Val1019Serfs*10) - - - COL5A2_00032 - - dbSNP Unknown Unknown This variant is incorrectly described as c.3050_3051insA in dbSNP and the predicted amino acid "substitution" is wrong. In addition, the frameshift predicted by this variant would be expected to be pathogenic: a null allele. The dbSNP data concerning this variant need to be treated with caution. -
+/+ 44 c.3104_3109del - - Deletion In-frame deletion/insertion p.(Gly1035_Pro1037delinsAla) - - - COL5A2_00044 AN_001952 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA PCR, SEQ - -
+/+ 44i c.3148-2A>G - NM_000393.2:c.3139-2A>G Substitution Splice site - - - - COL5A2_00017 EDS6 Classical EDS Malfait et al., 2005 DNA, RNA DHPLC, PCR, RT-PCR, SEQ, CSGE, SSCP - -
?/+ 47 c.3348dupG dbSNP - Duplication Frameshift p.(Lys1117Glufs*13) - - - COL5A2_00033 - - dbSNP Unknown Unknown This variant is incorrectly described as c.3345_3346insG in dbSNP and the predicted amino acid sequence outcome is wrong. In addition, the frameshift predicted by this variant would be expected to be pathogenic: a null allele. The dbSNP data concerning this variant need to be treated with caution. -
?/- 48 c.3411C>T dbSNP - Substitution Silent p.(=) - - - COL5A2_00034 - - dbSNP Unknown Unknown - -
+/+ 48 c.3437G>C - - Substitution Missense p.(Gly1146Ala) - - - COL5A2_00001 P4 Classical EDS Mitchell et al., 2009 DNA, RNA PCR, RT-PCR, SEQ, HA - -
+/+ 48 c.3445G>C - - Substitution Missense p.(Gly1149Arg) - - - COL5A2_00006 II-2 EDS II Richards et al., 1998 RNA RT-PCR, SEQ - -
+/+ 48 c.3445G>T - - Substitution Missense p.(Gly1149Cys) - - - COL5A2_00055 AN_005310 Classical EDS Weerakkody et al., 2016, Imperial College London, UK DNA HTS skin fragility, skin hyper-extensibility together with joint hypermobility Patient ID 62. Caucasian
+/+ 50 c.3526G>C - - Substitution Missense p.(Gly1176Arg) - - - COL5A2_00049 AN_002538 Classical EDS Italy:Brescia DNA PCR, SEQ This is a sporadic case (de novo mutation verified). Italian
+/+ 50 c.3625G>A - - Substitution Missense p.(Gly1209Arg) - - - COL5A2_00045 AN_001953 Classical EDS Symoens et al., 2012, Belgium:Ghent DNA PCR, SEQ - -
+/+ 51 c.3644G>T - - Substitution Missense p.Gly1215Val - - - COL5A2_00059 EDS11021711 Classical EDS Switzerland:Zurich DNA CNGP Collagen biochemical analysis showed abnormal overmodification and intracellular retention of type V collagen Malaysian
-/- 51 c.3689C>G - - Substitution Missense p.(Thr1230Arg) - - - COL5A2_00003 No. 20 - Grond-Ginsbach et al., 2002 Unknown Unknown This variant was originally mistakenly described as resulting in a Thr to Ser subsitution. The author has confirmed that it should be Thr to Arg. This mutation was previously described as c.3837C>G The variant is recorded in dbSNP. -
-/- 51 c.3690A>C - - Substitution Silent p.(=) - - - COL5A2_00010 - - Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP This mutation was originally described as an A>C substitution in NM_000393.2 at position 3838 counting from the start of the sequence. This variant is recorded in dbSNP. However, the information in dbSNP is muddled. Care! Caucasian
-/- 51 c.3720T>C - - Substitution Silent p.(=) - - - COL5A2_00011 - - Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP This mutation was originally described as a T>C substitution in NM_000393.2 at position 3868 counting from the start of the sequence. This variant is recorded in dbSNP. Caucasian
?/- 52 c.3969A>C dbSNP - Substitution Silent p.(=) - - - COL5A2_00035 - - dbSNP Unknown Unknown - -
-/? 53 c.4240G>A - - Substitution Missense p.(Asp1414Asn) - - - COL5A2_00012 - - Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP This mutation was originally described as a G>A substitution in NM_000393.2 at position 4388 counting from the start of the sequence. This variant is reported as being silent, but it actually results in a missense substitution. Caucasian
-/- 53 c.4295A>T - - Substitution Missense p.(Asp1432Val) - - - COL5A2_00009 - - Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP This mutation was originally described as an A>T substitution in NM_000393.2 at position 4443 counting from the start of the sequence. Caucasian
+/+ 53 c.4298delT - NM_000393.2:c.4289delT Deletion Frameshift p.(Ile1433Thrfs*43) - - - COL5A2_00014 EDS5 Classical EDS Malfait et al., 2005 DNA, RNA DHPLC, PCR, RT-PCR, SEQ, CSGE, SSCP The variant in this patient is described as leading to p.I1430fsx43 in the published account. -
?/-? 54 c.4362T>A - - Substitution Missense p.(Asn1454Lys) - - - COL5A2_00058 00050 EDS I United States:Fort Lee DNA SEQ It's not clear that the patient's COL5A2 variant is necessarily the cause of the EDS I phenotype. Filipino
?/- 54 c.4453A>T dbSNP - Substitution Missense p.(Thr1485Ser) - - - COL5A2_00036 - - dbSNP Unknown Unknown - -
-?/-? 54 c.4468G>A - - Substitution Missense p.(Gly1490Ser) - - - COL5A2_00056 Patient 10 TAAD Ziganshin et al., 2015 DNA WES The proband had aneurysm of the ascending aorta. -
-/- 54 c.*298G>A - - Substitution Other - - - - COL5A2_00013 - - Grond-Ginsbach et al., 2002 DNA, RNA PCR, RT-PCR, SEQ, SSCP This mutation was originally described as a G>A substitution in NM_000393.2 at position 4946 counting from the start of the sequence. Caucasian
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Legend: [ COL5A2 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 Legacy DNA change: Legacy DNA change Type: Type of variant at DNA level. Mutation Effect: Mutation effect at protein or RNA level. Protein: Variation at protein level. RNA change: Variation at RNA-level, (?) unknown but probably identical to DNA. Re-site: Variant creates (+) or destroys (-) a restriction enzyme recognition site. Frequency: Frequency if variant is non pathogenic. COL5A2 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