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: ENST00000696539
Querying Taster for transcript #2: ENST00000696533
Querying Taster for transcript #3: ENST00000320339
Querying Taster for transcript #4: ENST00000644802
Querying Taster for transcript #5: ENST00000536133
MT speed 0.43 s - this script 2.796514 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000320339	STEEP1	Deleterious	54\|46	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000536133	STEEP1	Deleterious	54\|46	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000696539	UBE2A	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000696533	UBE2A	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000644802(MANE Select)	STEEP1	Benign	45\|55	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes

MutationT@ster 2025

Variant:

23:119544489C>T_3_ENST00000320339

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Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:119544489C>T (GRCh38)

Gene symbol

STEEP1

Gene constraints

no data

Ensembl transcript ID

ENST00000320339.8

Genbank transcript ID

NM_001170569 (by similarity)

UniProt / AlphaMissense peptide

STEEP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.140G>A
g.20921G>A

AA changes

AAE:	C47Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		47	I	E	R	Q	Y	R	K	K	C	A	K	C	G	L	P	L	F	Y	Q	S	Q	P	K	N
mutated	not conserved	47	I	E	R	Q	Y	R	K	K	C	A	K	Y	G	L	P	L	F	Y	Q	S	Q	P	K
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	222	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	20918	wt: 8.60 / mu: 8.34	-	wt: gtcattgcag\|GTGTGGACTG mu: gtcattgcag\|GTATGGACTG

Distance from splice site

3

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

23

Strand

-1

Original gDNA sequence snippet

TTCACTGTGTCATTGCAGGTGTGGACTGCCGCTCTTCTACC

Altered gDNA sequence snippet

TTCACTGTGTCATTGCAGGTATGGACTGCCGCTCTTCTACC

Original cDNA sequence snippet

CAGGAAGAAATGTGCAAAGTGTGGACTGCCGCTCTTCTACC

Altered cDNA sequence snippet

CAGGAAGAAATGTGCAAAGTATGGACTGCCGCTCTTCTACC

Wildtype AA sequence

MRPRDRSRVI DAAKHAHKFC NTEDEETMYL RRPEGIERQY RKKCAKCGLP LFYQSQPKNA
PVTFIVDGAV VKFGQGFGKT NIYTQKQEPP KKVMMTKRTK DMGKFSSVTV STIDEEEEEI
EAREVADSYA QNAKVIEKQL ERKGMSKRRL QELAELEAKK AKMKGTLIDN QFK*

Mutated AA sequence

MRPRDRSRVI DAAKHAHKFC NTEDEETMYL RRPEGIERQY RKKCAKYGLP LFYQSQPKNA
PVTFIVDGAV VKFGQGFGKT NIYTQKQEPP KKVMMTKRTK DMGKFSSVTV STIDEEEEEI
EAREVADSYA QNAKVIEKQL ERKGMSKRRL QELAELEAKK AKMKGTLIDN QFK*

Position of stopcodon in wt / mu CDS

522 / 522

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

174 / 174

Position of stopcodon in wt / mu cDNA

794 / 794

Position of start ATG in wt / mu cDNA

273 / 273

Last intron/exon boundary

731

Theoretical NMD boundary in CDS

408

Length of CDS

522

Coding sequence (CDS) position

140

cDNA position

412

gDNA position

20921

Chromosomal position

119544489

Speed

0.14 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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MutationT@ster 2025

Variant:

23:119544489C>T_5_ENST00000536133

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Prediction:

DeleteriousPermalink

Summary:

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

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:119544489C>T (GRCh38)

Gene symbol

STEEP1

Gene constraints

no data

Ensembl transcript ID

ENST00000536133.2

Genbank transcript ID

NM_001170570 (by similarity)

UniProt / AlphaMissense peptide

STEEP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.245G>A
g.20921G>A

AA changes

AAE:	C82Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		82	T	E	D	E	E	T	M	Y	L	R	R	C	G	L	P	L	F	Y	Q	S	Q	P	K	N
mutated	not conserved	82	T	E	D	E	E	T	M	Y	L	R	R	Y	G	L	P	L	F	Y	Q	S	Q	P	K
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	222	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	20918	wt: 8.60 / mu: 8.34	-	wt: gtcattgcag\|GTGTGGACTG mu: gtcattgcag\|GTATGGACTG

Distance from splice site

3

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

23

Strand

-1

Original gDNA sequence snippet

TTCACTGTGTCATTGCAGGTGTGGACTGCCGCTCTTCTACC

Altered gDNA sequence snippet

TTCACTGTGTCATTGCAGGTATGGACTGCCGCTCTTCTACC

Original cDNA sequence snippet

GACTATGTATCTGCGGAGGTGTGGACTGCCGCTCTTCTACC

Altered cDNA sequence snippet

GACTATGTATCTGCGGAGGTATGGACTGCCGCTCTTCTACC

Wildtype AA sequence

MPKVVSRSVV CSDTRDREEY DDGEKPLHVY YCLCGQMVLV LDCQLEKLPM RPRDRSRVID
AAKHAHKFCN TEDEETMYLR RCGLPLFYQS QPKNAPVTFI VDGAVVKFGQ GFGKTNIYTQ
KQEPPKKVMM TKRTKDMGKF SSVTVSTIDE EEEEIEAREV ADSYAQNAKV IEKQLERKGM
SKRRLQELAE LEAKKAKMKG TLIDNQFK*

Mutated AA sequence

MPKVVSRSVV CSDTRDREEY DDGEKPLHVY YCLCGQMVLV LDCQLEKLPM RPRDRSRVID
AAKHAHKFCN TEDEETMYLR RYGLPLFYQS QPKNAPVTFI VDGAVVKFGQ GFGKTNIYTQ
KQEPPKKVMM TKRTKDMGKF SSVTVSTIDE EEEEIEAREV ADSYAQNAKV IEKQLERKGM
SKRRLQELAE LEAKKAKMKG TLIDNQFK*

Position of stopcodon in wt / mu CDS

627 / 627

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

209 / 209

Position of stopcodon in wt / mu cDNA

680 / 680

Position of start ATG in wt / mu cDNA

54 / 54

Last intron/exon boundary

617

Theoretical NMD boundary in CDS

513

Length of CDS

627

Coding sequence (CDS) position

245

cDNA position

298

gDNA position

20921

Chromosomal position

119544489

Speed

0.12 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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MutationT@ster 2025

Variant:

23:119544489C>T_1_ENST00000696539

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:119544489C>T (GRCh38)

Gene symbol

UBE2A

Gene constraints

no data

Ensembl transcript ID

ENST00000696539.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-376+1838C>T
g.69688C>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 'T' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

23

Strand

1

Original gDNA sequence snippet

GGTAGAAGAGCGGCAGTCCACACCTGCAATGACACAGTGAA

Altered gDNA sequence snippet

GGTAGAAGAGCGGCAGTCCATACCTGCAATGACACAGTGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MWFQSQIVGS APVYTGVVLS RRQTDPRLRR GSAVPLGASA SPSPASPASS ASSPAAGTRD
PSVCPTPDPA RDMSTPARRR LMRDFKRLQE DPPAGVSGAP SENNIMVWNA VIFGPEGTPF
EDGTFKLTIE FTEEYPNKPP TVRFVSKMFH PNVYADGSIC LDILQNRWSP TYDVSSILTS
IQSLLDEPNP NSPANSQAAQ LYQENKREYE KRVSAIVEQS WRDC*

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

581 / 581

Last intron/exon boundary

1126

Theoretical NMD boundary in CDS

495

Length of CDS

675

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

69688

Chromosomal position

119544489

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

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MutationT@ster 2025

Variant:

23:119544489C>T_2_ENST00000696533

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:119544489C>T (GRCh38)

Gene symbol

UBE2A

Gene constraints

no data

Ensembl transcript ID

ENST00000696533.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-157-29154C>T
g.69688C>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 'T' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

23

Strand

1

Original gDNA sequence snippet

GGTAGAAGAGCGGCAGTCCACACCTGCAATGACACAGTGAA

Altered gDNA sequence snippet

GGTAGAAGAGCGGCAGTCCATACCTGCAATGACACAGTGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MWFQSQIVGS APVYTGVVLS RRQTDPRLRR GSAVPLGASA SPSPASPASS ASSPAAGTRD
PSVCPTPDPA RDMSTPARRR LMRDFKRLQE DPPAGVSGAP SENNIMVWNA VIFGPEGTPF
EDGTFKLTIE FTEEYPNKPP TVRFVSKMFH PNVYADGSIC LDILQNRWSP TYDVSSILTS
IQSLLDEPNP NSPANSQAAQ LYQENKREYE KRVSAIVEQS WRDC*

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

251 / 251

Last intron/exon boundary

796

Theoretical NMD boundary in CDS

495

Length of CDS

675

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

69688

Chromosomal position

119544489

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

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MutationT@ster 2025

Variant:

23:119544489C>T_4_ENST00000644802

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Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 45|55 (del | benign) ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:119544489C>T (GRCh38)

Gene symbol

STEEP1

Gene constraints

no data

Ensembl transcript ID

ENST00000644802.2

Genbank transcript ID

NM_022101 (exact from MANE)

UniProt / AlphaMissense peptide

STEEP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.287G>A
g.20921G>A

AA changes

AAE:	C96Y	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		96	I	E	R	Q	Y	R	K	K	C	A	K	C	G	L	P	L	F	Y	Q	S	Q	P	K	N
mutated	not conserved	96	I	E	R	Q	Y	R	K	K	C	A	K	Y	G	L	P	L	F	Y	Q	S	Q	P	K
Ptroglodytes	all identical	96	-	-	R	N	S	L	C	H	C	-	R	C	G	L	P	L	F	Y	Q	S	Q	P	K
Mmulatta	no homologue
Fcatus	all identical	96	I	E	R	Q	Y	R	K	K	C	A	K	C	G	L	P	L	F	Y	Q	S	Q	P	K
Mmusculus	all identical	96	I	E	R	Q	Y	R	K	K	C	A	K	C	G	L	P	L	F	Y	Q	S	Q	P	K
Ggallus	all identical	96	I	E	R	Q	F	R	K	K	C	G	K	C	G	L	L	L	F	Y	Q	H	Q	Q	K
Trubripes	all identical	96	I	E	R	Q	Y	R	K	K	C	G	K	C	G	L	L	L	F	Y	Q	H	Q	E	K
Drerio	no homologue
Dmelanogaster	all identical	95	I	E	K	Q	Y	R	Y	K	C	R	S	C	S	L	P	L	Y	Y	R	H	S	P	-
Celegans	all identical	109	L	E	Q	Q	Y	R	K	M	C	K	K	C	S	I	P	L	F	Y	Q	-	H	P	S
Xtropicalis	all identical	96	I	E	R	Q	Y	R	K	K	C	S	K	C	S	L	L	L	F	Y	Q	H	S	Q	K

Protein features

Start (aa)	End (aa)	Feature	Details
1	222	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	20918	wt: 8.60 / mu: 8.34	-	wt: gtcattgcag\|GTGTGGACTG mu: gtcattgcag\|GTATGGACTG

Distance from splice site

3

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

23

Strand

-1

Original gDNA sequence snippet

TTCACTGTGTCATTGCAGGTGTGGACTGCCGCTCTTCTACC

Altered gDNA sequence snippet

TTCACTGTGTCATTGCAGGTATGGACTGCCGCTCTTCTACC

Original cDNA sequence snippet

CAGGAAGAAATGTGCAAAGTGTGGACTGCCGCTCTTCTACC

Altered cDNA sequence snippet

CAGGAAGAAATGTGCAAAGTATGGACTGCCGCTCTTCTACC

Wildtype AA sequence

MPKVVSRSVV CSDTRDREEY DDGEKPLHVY YCLCGQMVLV LDCQLEKLPM RPRDRSRVID
AAKHAHKFCN TEDEETMYLR RPEGIERQYR KKCAKCGLPL FYQSQPKNAP VTFIVDGAVV
KFGQGFGKTN IYTQKQEPPK KVMMTKRTKD MGKFSSVTVS TIDEEEEEIE AREVADSYAQ
NAKVIEKQLE RKGMSKRRLQ ELAELEAKKA KMKGTLIDNQ FK*

Mutated AA sequence

MPKVVSRSVV CSDTRDREEY DDGEKPLHVY YCLCGQMVLV LDCQLEKLPM RPRDRSRVID
AAKHAHKFCN TEDEETMYLR RPEGIERQYR KKCAKYGLPL FYQSQPKNAP VTFIVDGAVV
KFGQGFGKTN IYTQKQEPPK KVMMTKRTKD MGKFSSVTVS TIDEEEEEIE AREVADSYAQ
NAKVIEKQLE RKGMSKRRLQ ELAELEAKKA KMKGTLIDNQ FK*

Position of stopcodon in wt / mu CDS

669 / 669

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

223 / 223

Position of stopcodon in wt / mu cDNA

723 / 723

Position of start ATG in wt / mu cDNA

55 / 55

Last intron/exon boundary

660

Theoretical NMD boundary in CDS

555

Length of CDS

669

Coding sequence (CDS) position

287

cDNA position

341

gDNA position

20921

Chromosomal position

119544489

Speed

0.13 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