Results

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000328300
Querying Taster for transcript #2: ENST00000361603
MT speed 0.03 s - this script 2.413985 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000328300(MANE Select)	COL4A5	Deleterious	96\|104	without_aae		No	Yes			Single base exchange		N/A	Known disease mutation: ClinVar ID 2138707 (pathogenic) Splice site lost
ENST00000361603	COL4A5	Deleterious	96\|104	without_aae		No	Yes			Single base exchange		N/A	Known disease mutation: ClinVar ID 2138707 (pathogenic) Splice site lost

Variant:

23:108668317A>G_1_ENST00000328300

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2138707 (pathogenic)
Splice site lost

Model: without_aae
Tree vote: 96|104 (del | benign) ?
Automatic classification due to ClinVar,
tree vote conflicts with the automatic classification ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:108668317A>G (GRCh38)

Gene symbol

COL4A5

Gene constraints

no data

Ensembl transcript ID

ENST00000328300.11

Genbank transcript ID

NM_033380 (exact from MANE)

UniProt / AlphaMissense peptide

CO4A5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.3605-2A>G
g.228480A>G

AA changes

N/A

Frameshift

Length of protein

N/A

Pathogenic variant (ClinVar)

not provided

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	228481	wt: 0.00 / mu: 0.00	-	wt: actttcatag\|GCCAAAAGGG mu: actttcatgg\|GCCAAAAGGG

Distance from splice site

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

Strand

Original gDNA sequence snippet

TAATTATACTTTACTTTCATAGGCCAAAAGGGTGATGGAGG

Altered gDNA sequence snippet

TAATTATACTTTACTTTCATGGGCCAAAAGGGTGATGGAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLRGVSLAA GLFLLALSLW GQPAEAAACY GCSPGSKCDC SGIKGEKGER GFPGLEGHPG
LPGFPGPEGP PGPRGQKGDD GIPGPPGPKG IRGPPGLPGF PGTPGLPGMP GHDGAPGPQG
IPGCNGTKGE RGFPGSPGFP GLQGPPGPPG IPGMKGEPGS IIMSSLPGPK GNPGYPGPPG
IQGLPGPTGI PGPIGPPGPP GLMGPPGPPG LPGPKGNMGL NFQGPKGEKG EQGLQGPPGP
PGQISEQKRP IDVEFQKGDQ GLPGDRGPPG PPGIRGPPGP PGGEKGEKGE QGEPGKRGKP
GKDGENGQPG IPGLPGDPGY PGEPGRDGEK GQKGDTGPPG PPGLVIPRPG TGITIGEKGN
IGLPGLPGEK GERGFPGIQG PPGLPGPPGA AVMGPPGPPG FPGERGQKGD EGPPGISIPG
PPGLDGQPGA PGLPGPPGPA GPHIPPSDEI CEPGPPGPPG SPGDKGLQGE QGVKGDKGDT
CFNCIGTGIS GPPGQPGLPG LPGPPGSLGF PGQKGEKGQA GATGPKGLPG IPGAPGAPGF
PGSKGEPGDI LTFPGMKGDK GELGSPGAPG LPGLPGTPGQ DGLPGLPGPK GEPGGITFKG
ERGPPGNPGL PGLPGNIGPM GPPGFGPPGP VGEKGIQGVA GNPGQPGIPG PKGDPGQTIT
QPGKPGLPGN PGRDGDVGLP GDPGLPGQPG LPGIPGSKGE PGIPGIGLPG PPGPKGFPGI
PGPPGAPGTP GRIGLEGPPG PPGFPGPKGE PGFALPGPPG PPGLPGFKGA LGPKGDRGFP
GPPGPPGRTG LDGLPGPKGD VGPNGQPGPM GPPGLPGIGV QGPPGPPGIP GPIGQPGLHG
IPGEKGDPGP PGLDVPGPPG ERGSPGIPGA PGPIGPPGSP GLPGKAGASG FPGTKGEMGM
MGPPGPPGPL GIPGRSGVPG LKGDDGLQGQ PGLPGPTGEK GSKGEPGLPG PPGPMDPNLL
GSKGEKGEPG LPGIPGVSGP KGYQGLPGDP GQPGLSGQPG LPGPPGPKGN PGLPGQPGLI
GPPGLKGTIG DMGFPGPQGV EGPPGPSGVP GQPGSPGLPG QKGDKGDPGI SSIGLPGLPG
PKGEPGLPGY PGNPGIKGSV GDPGLPGLPG TPGAKGQPGL PGFPGTPGPP GPKGISGPPG
NPGLPGEPGP VGGGGHPGQP GPPGEKGKPG QDGIPGPAGQ KGEPGQPGFG NPGPPGLPGL
SGQKGDGGLP GIPGNPGLPG PKGEPGFHGF PGVQGPPGPP GSPGPALEGP KGNPGPQGPP
GRPGPTGFQG LPGPEGPPGL PGNGGIKGEK GNPGQPGLPG LPGLKGDQGP PGLQGNPGRP
GLNGMKGDPG LPGVPGFPGM KGPSGVPGSA GPEGEPGLIG PPGPPGLPGP SGQSIIIKGD
AGPPGIPGQP GLKGLPGPQG PQGLPGPTGP PGDPGRNGLP GFDGAGGRKG DPGLPGQPGT
RGLDGPPGPD GLQGPPGPPG TSSVAHGFLI TRHSQTTDAP QCPQGTLQVY EGFSLLYVQG
NKRAHGQDLG TAGSCLRRFS TMPFMFCNIN NVCNFASRND YSYWLSTPEP MPMSMQPLKG
QSIQPFISRC AVCEAPAVVI AVHSQTIQIP HCPQGWDSLW IGYSFMMHTS AGAEGSGQAL
ASPGSCLEEF RSAPFIECHG RGTCNYYANS YSFWLATVDV SDMFSKPQSE TLKAGDLRTR
ISRCQVCMKR T*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

289 / 289

Last intron/exon boundary

5282

Theoretical NMD boundary in CDS

4943

Length of CDS

5076

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

228480

Chromosomal position

108668317

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

Variant:

23:108668317A>G_2_ENST00000361603

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2138707 (pathogenic)
Splice site lost

Model: without_aae
Tree vote: 96|104 (del | benign) ?
Automatic classification due to ClinVar,
tree vote conflicts with the automatic classification ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:108668317A>G (GRCh38)

Gene symbol

COL4A5

Gene constraints

no data

Ensembl transcript ID

ENST00000361603.7

Genbank transcript ID

NM_000495 (by similarity)

UniProt / AlphaMissense peptide

CO4A5_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.3605-2A>G
g.228480A>G

AA changes

N/A

Frameshift

Length of protein

N/A

Pathogenic variant (ClinVar)

not provided

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	228481	wt: 0.00 / mu: 0.00	-	wt: actttcatag\|GCCAAAAGGG mu: actttcatgg\|GCCAAAAGGG

Distance from splice site

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

Strand

Original gDNA sequence snippet

TAATTATACTTTACTTTCATAGGCCAAAAGGGTGATGGAGG

Altered gDNA sequence snippet

TAATTATACTTTACTTTCATGGGCCAAAAGGGTGATGGAGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MKLRGVSLAA GLFLLALSLW GQPAEAAACY GCSPGSKCDC SGIKGEKGER GFPGLEGHPG
LPGFPGPEGP PGPRGQKGDD GIPGPPGPKG IRGPPGLPGF PGTPGLPGMP GHDGAPGPQG
IPGCNGTKGE RGFPGSPGFP GLQGPPGPPG IPGMKGEPGS IIMSSLPGPK GNPGYPGPPG
IQGLPGPTGI PGPIGPPGPP GLMGPPGPPG LPGPKGNMGL NFQGPKGEKG EQGLQGPPGP
PGQISEQKRP IDVEFQKGDQ GLPGDRGPPG PPGIRGPPGP PGGEKGEKGE QGEPGKRGKP
GKDGENGQPG IPGLPGDPGY PGEPGRDGEK GQKGDTGPPG PPGLVIPRPG TGITIGEKGN
IGLPGLPGEK GERGFPGIQG PPGLPGPPGA AVMGPPGPPG FPGERGQKGD EGPPGISIPG
PPGLDGQPGA PGLPGPPGPA GPHIPPSDEI CEPGPPGPPG SPGDKGLQGE QGVKGDKGDT
CFNCIGTGIS GPPGQPGLPG LPGPPGSLGF PGQKGEKGQA GATGPKGLPG IPGAPGAPGF
PGSKGEPGDI LTFPGMKGDK GELGSPGAPG LPGLPGTPGQ DGLPGLPGPK GEPGGITFKG
ERGPPGNPGL PGLPGNIGPM GPPGFGPPGP VGEKGIQGVA GNPGQPGIPG PKGDPGQTIT
QPGKPGLPGN PGRDGDVGLP GDPGLPGQPG LPGIPGSKGE PGIPGIGLPG PPGPKGFPGI
PGPPGAPGTP GRIGLEGPPG PPGFPGPKGE PGFALPGPPG PPGLPGFKGA LGPKGDRGFP
GPPGPPGRTG LDGLPGPKGD VGPNGQPGPM GPPGLPGIGV QGPPGPPGIP GPIGQPGLHG
IPGEKGDPGP PGLDVPGPPG ERGSPGIPGA PGPIGPPGSP GLPGKAGASG FPGTKGEMGM
MGPPGPPGPL GIPGRSGVPG LKGDDGLQGQ PGLPGPTGEK GSKGEPGLPG PPGPMDPNLL
GSKGEKGEPG LPGIPGVSGP KGYQGLPGDP GQPGLSGQPG LPGPPGPKGN PGLPGQPGLI
GPPGLKGTIG DMGFPGPQGV EGPPGPSGVP GQPGSPGLPG QKGDKGDPGI SSIGLPGLPG
PKGEPGLPGY PGNPGIKGSV GDPGLPGLPG TPGAKGQPGL PGFPGTPGPP GPKGISGPPG
NPGLPGEPGP VGGGGHPGQP GPPGEKGKPG QDGIPGPAGQ KGEPGQPGFG NPGPPGLPGL
SGQKGDGGLP GIPGNPGLPG PKGEPGFHGF PGVQGPPGPP GSPGPALEGP KGNPGPQGPP
GRPGLPGPEG PPGLPGNGGI KGEKGNPGQP GLPGLPGLKG DQGPPGLQGN PGRPGLNGMK
GDPGLPGVPG FPGMKGPSGV PGSAGPEGEP GLIGPPGPPG LPGPSGQSII IKGDAGPPGI
PGQPGLKGLP GPQGPQGLPG PTGPPGDPGR NGLPGFDGAG GRKGDPGLPG QPGTRGLDGP
PGPDGLQGPP GPPGTSSVAH GFLITRHSQT TDAPQCPQGT LQVYEGFSLL YVQGNKRAHG
QDLGTAGSCL RRFSTMPFMF CNINNVCNFA SRNDYSYWLS TPEPMPMSMQ PLKGQSIQPF
ISRCAVCEAP AVVIAVHSQT IQIPHCPQGW DSLWIGYSFM MHTSAGAEGS GQALASPGSC
LEEFRSAPFI ECHGRGTCNY YANSYSFWLA TVDVSDMFSK PQSETLKAGD LRTRISRCQV
CMKRT*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

203 / 203

Last intron/exon boundary

5178

Theoretical NMD boundary in CDS

4925

Length of CDS

5058

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

228480

Chromosomal position

108668317

Speed

0.01 s

MutationT@ster 2025

Transcript summary:

MutationT@ster 2025

Variant:

23:108668317A>G_1_ENST00000328300

Prediction:

Summary:

MutationT@ster 2025

Variant:

23:108668317A>G_2_ENST00000361603

Prediction:

Summary: