MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000621271
Querying Taster for transcript #2: ENST00000427926
MT speed 0.05 s - this script 2.372282 s

Transcript summary:

Permalink

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
ENST00000621271	CLTCL1	Deleterious	198\|2	without_aae		No				Single base exchange		N/A	Splice site lost
ENST00000427926(MANE Select)	CLTCL1	Deleterious	199\|1	without_aae		No				Single base exchange		N/A	Splice site lost

MutationT@ster 2025

Variant:

22:19225452C>A_1_ENST00000621271

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 198|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr22:19225452C>A (GRCh38)

Gene symbol

CLTCL1

Gene constraints

LOEUF: 1.01, LOF (oe): 0.89, misssense (oe): 0.91, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000621271.4

Genbank transcript ID

NM_001835 (by similarity)

UniProt / AlphaMissense peptide

CLH2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2128+1G>T
g.66268G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

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

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.466	1
	7.198	1
(flanking)	7.198	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	66267	wt: 0.00 / mu: 0.00	-	wt: AGTTACAAAG\|gtaaaccatg mu: AGTTACAAAG\|ttaaaccatg

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

22

Strand

-1

Original gDNA sequence snippet

ATCCTTCAAGAGTTACAAAGGTAAACCATGCAGCCTCTCGC

Altered gDNA sequence snippet

ATCCTTCAAGAGTTACAAAGTTAAACCATGCAGCCTCTCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAQILPVRFQ EHFQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV TIIDMSDPMA
PIRRPISAES AIMNPASKVI ALKAGKTLQI FNIEMKSKMK AHTMAEEVIF WKWVSVNTVA
LVTETAVYHW SMEGDSQPMK MFDRHTSLVG CQVIHYRTDE YQKWLLLVGI SAQQNRVVGA
MQLYSVDRKV SQPIEGHAAA FAEFKMEGNA KPATLFCFAV RNPTGGKLHI IEVGQPAAGN
QPFVKKAVDV FFPPEAQNDF PVAMQIGAKH GVIYLITKYG YLHLYDLESG VCICMNRISA
DTIFVTAPHK PTSGIIGVNK KGQVLSVCVE EDNIVNYATN VLQNPDLGLR LAVRSNLAGA
EKLFVRKFNT LFAQGSYAEA AKVAASAPKG ILRTRETVQK FQSIPAQSGQ ASPLLQYFGI
LLDQGQLNKL ESLELCHLVL QQGRKQLLEK WLKEDKLECS EELGDLVKTT DPMLALSVYL
RANVPSKVIQ CFAETGQFQK IVLYAKKVGY TPDWIFLLRG VMKISPEQGL QFSRMLVQDE
EPLANISQIV DIFMENSLIQ QCTSFLLDAL KNNRPAEGLL QTWLLEMNLV HAPQVADAIL
GNKMFTHYDR AHIAQLCEKA GLLQQALEHY TDLYDIKRAV VHTHLLNPEW LVNFFGSLSV
EDSVECLHAM LSANIRQNLQ LCVQVASKYH EQLGTQALVE LFESFKSYKG LFYFLGSIVN
FSQDPDVHLK YIQAACKTGQ IKEVERICRE SSCYNPERVK NFLKEAKLTD QLPLIIVCDR
FGFVHDLVLY LYRNNLQRYI EIYVQKVNPS RTPAVIGGLL DVDCSEEVIK HLIMAVRGQF
STDELVAEVE KRNRLKLLLP WLESQIQEGC EEPATHNALA KIYIDSNNSP ECFLRENAYY
DSSVVGRYCE KRDPHLACVA YERGQCDLEL IKVCNENSLF KSEARYLVCR KDPELWAHVL
EETNPSRRQL IDQVVQTALS ETRDPEEISV TVKAFMTADL PNELIELLEK IVLDNSVFSE
HRNLQNLLIL TAIKADRTRV MEYISRLDNY DALDIASIAV SSALYEEAFT VFHKFDMNAS
AIQVLIEHIG NLDRAYEFAE RCNEPAVWSQ LAQAQLQKDL VKEAINSYIR GDDPSSYLEV
VQSASRSNNW EDLVKFLQMA RKKGRESYIE TELIFALAKT SRVSELEDFI NGPNNAHIQQ
VGDRCYEEGM YEAAKLLYSN VSNFARLAST LVHLGEYQAA VDNSRKASST RTWKEVCFAC
MDGQEFRFAQ LCGLHIVIHA DELEELMCYY QDRGYFEELI LLLEAALGLE RAHMGMFTEL
AILYSKFKPQ KMLEHLELFW SRVNIPKVLR AAEQAHLWAE LVFLYDKYEE YDNAVLTMMS
HPTEAWKEGQ FKDIITKVAN VELCYRALQF YLDYKPLLIN DLLLVLSPRL DHTWTVSFFS
KAGQLPLVKP YLRSVQSHNN KSVNEALNHL LTEEEDYQDA MQHAAESRDA ELAQKLLQWF
LEEGKRECFA ACLFTCYDLL RPDMVLELAW RHNLVDLAMP YFIQVMREYL SKVDKLDALE
SLRKQEEHVT EPAPLVFDFD GHE*

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

45 / 45

Last intron/exon boundary

4816

Theoretical NMD boundary in CDS

4721

Length of CDS

4752

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

66268

Chromosomal position

19225452

Speed

0.03 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

MutationT@ster 2025

Variant:

22:19225452C>A_2_ENST00000427926

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 199|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr22:19225452C>A (GRCh38)

Gene symbol

CLTCL1

Gene constraints

LOEUF: 0.99, LOF (oe): 0.87, misssense (oe): 0.91, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000427926.6

Genbank transcript ID

NM_007098 (exact from MANE)

UniProt / AlphaMissense peptide

CLH2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2128+1G>T
g.66268G>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

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

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.466	1
	7.198	1
(flanking)	7.198	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	66267	wt: 0.00 / mu: 0.00	-	wt: AGTTACAAAG\|gtaaaccatg mu: AGTTACAAAG\|ttaaaccatg

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

22

Strand

-1

Original gDNA sequence snippet

ATCCTTCAAGAGTTACAAAGGTAAACCATGCAGCCTCTCGC

Altered gDNA sequence snippet

ATCCTTCAAGAGTTACAAAGTTAAACCATGCAGCCTCTCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAQILPVRFQ EHFQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV TIIDMSDPMA
PIRRPISAES AIMNPASKVI ALKAGKTLQI FNIEMKSKMK AHTMAEEVIF WKWVSVNTVA
LVTETAVYHW SMEGDSQPMK MFDRHTSLVG CQVIHYRTDE YQKWLLLVGI SAQQNRVVGA
MQLYSVDRKV SQPIEGHAAA FAEFKMEGNA KPATLFCFAV RNPTGGKLHI IEVGQPAAGN
QPFVKKAVDV FFPPEAQNDF PVAMQIGAKH GVIYLITKYG YLHLYDLESG VCICMNRISA
DTIFVTAPHK PTSGIIGVNK KGQVLSVCVE EDNIVNYATN VLQNPDLGLR LAVRSNLAGA
EKLFVRKFNT LFAQGSYAEA AKVAASAPKG ILRTRETVQK FQSIPAQSGQ ASPLLQYFGI
LLDQGQLNKL ESLELCHLVL QQGRKQLLEK WLKEDKLECS EELGDLVKTT DPMLALSVYL
RANVPSKVIQ CFAETGQFQK IVLYAKKVGY TPDWIFLLRG VMKISPEQGL QFSRMLVQDE
EPLANISQIV DIFMENSLIQ QCTSFLLDAL KNNRPAEGLL QTWLLEMNLV HAPQVADAIL
GNKMFTHYDR AHIAQLCEKA GLLQQALEHY TDLYDIKRAV VHTHLLNPEW LVNFFGSLSV
EDSVECLHAM LSANIRQNLQ LCVQVASKYH EQLGTQALVE LFESFKSYKG LFYFLGSIVN
FSQDPDVHLK YIQAACKTGQ IKEVERICRE SSCYNPERVK NFLKEAKLTD QLPLIIVCDR
FGFVHDLVLY LYRNNLQRYI EIYVQKVNPS RTPAVIGGLL DVDCSEEVIK HLIMAVRGQF
STDELVAEVE KRNRLKLLLP WLESQIQEGC EEPATHNALA KIYIDSNNSP ECFLRENAYY
DSSVVGRYCE KRDPHLACVA YERGQCDLEL IKVCNENSLF KSEARYLVCR KDPELWAHVL
EETNPSRRQL IDQVVQTALS ETRDPEEISV TVKAFMTADL PNELIELLEK IVLDNSVFSE
HRNLQNLLIL TAIKADRTRV MEYISRLDNY DALDIASIAV SSALYEEAFT VFHKFDMNAS
AIQVLIEHIG NLDRAYEFAE RCNEPAVWSQ LAQAQLQKDL VKEAINSYIR GDDPSSYLEV
VQSASRSNNW EDLVKFLQMA RKKGRESYIE TELIFALAKT SRVSELEDFI NGPNNAHIQQ
VGDRCYEEGM YEAAKLLYSN VSNFARLAST LVHLGEYQAA VDNSRKASST RTWKEVCFAC
MDGQEFRFAQ LCGLHIVIHA DELEELMCYY QDRGYFEELI LLLEAALGLE RAHMGMFTEL
AILYSKFKPQ KMLEHLELFW SRVNIPKVLR AAEQAHLWAE LVFLYDKYEE YDNAVLTMMS
HPTEAWKEGQ FKDIITKVAN VELCYRALQF YLDYKPLLIN DLLLVLSPRL DHTWTVSFFS
KAGQLPLVKP YLRSVQSHNN KSVNEALNHL LTEEEDYQGL RASIDAYDNF DNISLAQQLE
KHQLMEFRCI AAYLYKGNNW WAQSVELCKK DHLYKDAMQH AAESRDAELA QKLLQWFLEE
GKRECFAACL FTCYDLLRPD MVLELAWRHN LVDLAMPYFI QVMREYLSKV DKLDALESLR
KQEEHVTEPA PLVFDFDGHE *

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

79 / 79

Last intron/exon boundary

5021

Theoretical NMD boundary in CDS

4892

Length of CDS

4923

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

66268

Chromosomal position

19225452

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