MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000396578
MT speed 0.08 s - this script 2.544244 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
ENST00000396578(MANE Select)	COL4A3	Deleterious	79\|21	simple_aae		Yes				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes

MutationT@ster 2025

Variant:

2:227304019G>A_1_ENST00000396578

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:227304019G>A (GRCh38)

Gene symbol

COL4A3

Gene constraints

LOEUF: 0.71, LOF (oe): 0.61, misssense (oe): 0.85, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000396578.8

Genbank transcript ID

NM_000091 (exact from MANE)

UniProt / AlphaMissense peptide

CO4A3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4028G>A
g.139396G>A

AA changes

AAE:	G1343D	?
Score:	94

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		1343	P	P	G	P	I	G	P	K	G	P	P	G	V	R	G	D	P	G	T	L	K	I	I	S
mutated	not conserved	1343	P	P	G	P	I	G	P	K	G	P	P	D	V	R	G	D	P	G	T	L	K	I	I
Ptroglodytes	all identical	1343	P	P	G	P	I	G	P	K	G	L	P	G	V	R	G	D	P	G	T	L	K	I	I
Mmulatta	all identical	1343	P	P	G	P	I	G	P	I	G	P	P	G	I	R	G	D	P	G	T	L	K	I	I
Fcatus	all identical	1341	P	P	G	Q	I	G	P	K	G	P	P	G	I	R	G	D	P	G	T	V	K	I	I
Mmusculus	all identical	1341	H	P	G	P	V	G	P	K	G	P	P	G	P	R	G	K	P	G	T	L	K	V	I
Ggallus	all identical	1343	P	P	G	P	R	G	A	E	G	P	R	G	P	K	G	Q	P	GPPGV	S	E	R	I	F
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
29	1670	CHAIN		lost
43	1438	REGION	Triple-helical region	lost
502	1442	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.384	1
	4.023	1
(flanking)	-0.009	0.007

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	139395	wt: 9.87 / mu: 8.85	-	wt: atgtcaacag\|GTGTACGTGG mu: atgtcaacag\|ATGTACGTGG

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

2

Strand

1

Original gDNA sequence snippet

TCTTATGTTTATGTCAACAGGTGTACGTGGAGACCCTGGCA

Altered gDNA sequence snippet

TCTTATGTTTATGTCAACAGATGTACGTGGAGACCCTGGCA

Original cDNA sequence snippet

TGGGCCAAAAGGACCACCTGGTGTACGTGGAGACCCTGGCA

Altered cDNA sequence snippet

TGGGCCAAAAGGACCACCTGATGTACGTGGAGACCCTGGCA

Wildtype AA sequence

MSARTAPRPQ VLLLPLLLVL LAAAPAASKG CVCKDKGQCF CDGAKGEKGE KGFPGPPGSP
GQKGFTGPEG LPGPQGPKGF PGLPGLTGSK GVRGISGLPG FSGSPGLPGT PGNTGPYGLV
GVPGCSGSKG EQGFPGLPGT LGYPGIPGAA GLKGQKGAPA KEEDIELDAK GDPGLPGAPG
PQGLPGPPGF PGPVGPPGPP GFFGFPGAMG PRGPKGHMGE RVIGHKGERG VKGLTGPPGP
PGTVIVTLTG PDNRTDLKGE KGDKGAMGEP GPPGPSGLPG ESYGSEKGAP GDPGLQGKPG
KDGVPGFPGS EGVKGNRGFP GLMGEDGIKG QKGDIGPPGF RGPTEYYDTY QEKGDEGTPG
PPGPRGARGP QGPSGPPGVP GSPGSSRPGL RGAPGWPGLK GSKGERGRPG KDAMGTPGSP
GCAGSPGLPG SPGPPGPPGD IVFRKGPPGD HGLPGYLGSP GIPGVDGPKG EPGLLCTQCP
YIPGPPGLPG LPGLHGVKGI PGRQGAAGLK GSPGSPGNTG LPGFPGFPGA QGDPGLKGEK
GETLQPEGQV GVPGDPGLRG QPGRKGLDGI PGTPGVKGLP GPKGELALSG EKGDQGPPGD
PGSPGSPGPA GPAGPPGYGP QGEPGLQGTQ GVPGAPGPPG EAGPRGELSV STPVPGPPGP
PGPPGHPGPQ GPPGIPGSLG KCGDPGLPGP DGEPGIPGIG FPGPPGPKGD QGFPGTKGSL
GCPGKMGEPG LPGKPGLPGA KGEPAVAMPG GPGTPGFPGE RGNSGEHGEI GLPGLPGLPG
TPGNEGLDGP RGDPGQPGPP GEQGPPGRCI EGPRGAQGLP GLNGLKGQQG RRGKTGPKGD
PGIPGLDRSG FPGETGSPGI PGHQGEMGPL GQRGYPGNPG ILGPPGEDGV IGMMGFPGAI
GPPGPPGNPG TPGQRGSPGI PGVKGQRGTP GAKGEQGDKG NPGPSEISHV IGDKGEPGLK
GFAGNPGEKG NRGVPGMPGL KGLKGLPGPA GPPGPRGDLG STGNPGEPGL RGIPGSMGNM
GMPGSKGKRG TLGFPGRAGR PGLPGIHGLQ GDKGEPGYSE GTRPGPPGPT GDPGLPGDMG
KKGEMGQPGP PGHLGPAGPE GAPGSPGSPG LPGKPGPHGD LGFKGIKGLL GPPGIRGPPG
LPGFPGSPGP MGIRGDQGRD GIPGPAGEKG ETGLLRAPPG PRGNPGAQGA KGDRGAPGFP
GLPGRKGAMG DAGPRGPTGI EGFPGPPGLP GAIIPGQTGN RGPPGSRGSP GAPGPPGPPG
SHVIGIKGDK GSMGHPGPKG PPGTAGDMGP PGRLGAPGTP GLPGPRGDPG FQGFPGVKGE
KGNPGFLGSI GPPGPIGPKG PPGVRGDPGT LKIISLPGSP GPPGTPGEPG MQGEPGPPGP
PGNLGPCGPR GKPGKDGKPG TPGPAGEKGN KGSKGEPGPA GSDGLPGLKG KRGDSGSPAT
WTTRGFVFTR HSQTTAIPSC PEGTVPLYSG FSFLFVQGNQ RAHGQDLGTL GSCLQRFTTM
PFLFCNVNDV CNFASRNDYS YWLSTPALMP MNMAPITGRA LEPYISRCTV CEGPAIAIAV
HSQTTDIPPC PHGWISLWKG FSFIMFTSAG SEGTGQALAS PGSCLEEFRA SPFLECHGRG
TCNYYSNSYS FWLASLNPER MFRKPIPSTV KAGELEKIIS RCQVCMKKRH *

Mutated AA sequence

MSARTAPRPQ VLLLPLLLVL LAAAPAASKG CVCKDKGQCF CDGAKGEKGE KGFPGPPGSP
GQKGFTGPEG LPGPQGPKGF PGLPGLTGSK GVRGISGLPG FSGSPGLPGT PGNTGPYGLV
GVPGCSGSKG EQGFPGLPGT LGYPGIPGAA GLKGQKGAPA KEEDIELDAK GDPGLPGAPG
PQGLPGPPGF PGPVGPPGPP GFFGFPGAMG PRGPKGHMGE RVIGHKGERG VKGLTGPPGP
PGTVIVTLTG PDNRTDLKGE KGDKGAMGEP GPPGPSGLPG ESYGSEKGAP GDPGLQGKPG
KDGVPGFPGS EGVKGNRGFP GLMGEDGIKG QKGDIGPPGF RGPTEYYDTY QEKGDEGTPG
PPGPRGARGP QGPSGPPGVP GSPGSSRPGL RGAPGWPGLK GSKGERGRPG KDAMGTPGSP
GCAGSPGLPG SPGPPGPPGD IVFRKGPPGD HGLPGYLGSP GIPGVDGPKG EPGLLCTQCP
YIPGPPGLPG LPGLHGVKGI PGRQGAAGLK GSPGSPGNTG LPGFPGFPGA QGDPGLKGEK
GETLQPEGQV GVPGDPGLRG QPGRKGLDGI PGTPGVKGLP GPKGELALSG EKGDQGPPGD
PGSPGSPGPA GPAGPPGYGP QGEPGLQGTQ GVPGAPGPPG EAGPRGELSV STPVPGPPGP
PGPPGHPGPQ GPPGIPGSLG KCGDPGLPGP DGEPGIPGIG FPGPPGPKGD QGFPGTKGSL
GCPGKMGEPG LPGKPGLPGA KGEPAVAMPG GPGTPGFPGE RGNSGEHGEI GLPGLPGLPG
TPGNEGLDGP RGDPGQPGPP GEQGPPGRCI EGPRGAQGLP GLNGLKGQQG RRGKTGPKGD
PGIPGLDRSG FPGETGSPGI PGHQGEMGPL GQRGYPGNPG ILGPPGEDGV IGMMGFPGAI
GPPGPPGNPG TPGQRGSPGI PGVKGQRGTP GAKGEQGDKG NPGPSEISHV IGDKGEPGLK
GFAGNPGEKG NRGVPGMPGL KGLKGLPGPA GPPGPRGDLG STGNPGEPGL RGIPGSMGNM
GMPGSKGKRG TLGFPGRAGR PGLPGIHGLQ GDKGEPGYSE GTRPGPPGPT GDPGLPGDMG
KKGEMGQPGP PGHLGPAGPE GAPGSPGSPG LPGKPGPHGD LGFKGIKGLL GPPGIRGPPG
LPGFPGSPGP MGIRGDQGRD GIPGPAGEKG ETGLLRAPPG PRGNPGAQGA KGDRGAPGFP
GLPGRKGAMG DAGPRGPTGI EGFPGPPGLP GAIIPGQTGN RGPPGSRGSP GAPGPPGPPG
SHVIGIKGDK GSMGHPGPKG PPGTAGDMGP PGRLGAPGTP GLPGPRGDPG FQGFPGVKGE
KGNPGFLGSI GPPGPIGPKG PPDVRGDPGT LKIISLPGSP GPPGTPGEPG MQGEPGPPGP
PGNLGPCGPR GKPGKDGKPG TPGPAGEKGN KGSKGEPGPA GSDGLPGLKG KRGDSGSPAT
WTTRGFVFTR HSQTTAIPSC PEGTVPLYSG FSFLFVQGNQ RAHGQDLGTL GSCLQRFTTM
PFLFCNVNDV CNFASRNDYS YWLSTPALMP MNMAPITGRA LEPYISRCTV CEGPAIAIAV
HSQTTDIPPC PHGWISLWKG FSFIMFTSAG SEGTGQALAS PGSCLEEFRA SPFLECHGRG
TCNYYSNSYS FWLASLNPER MFRKPIPSTV KAGELEKIIS RCQVCMKKRH *

Position of stopcodon in wt / mu CDS

5013 / 5013

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

1671 / 1671

Position of stopcodon in wt / mu cDNA

5116 / 5116

Position of start ATG in wt / mu cDNA

104 / 104

Last intron/exon boundary

5031

Theoretical NMD boundary in CDS

4877

Length of CDS

5013

Coding sequence (CDS) position

4028

cDNA position

4131

gDNA position

139396

Chromosomal position

227304019

Speed

0.08 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

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