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: ENST00000296589
Querying Taster for transcript #2: ENST00000382102
Querying Taster for transcript #3: ENST00000509381
MT speed 0.17 s - this script 2.570537 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
ENST00000509381	SLC45A2	Deleterious	75\|25	3utr	No	Single base exchange	N/A
ENST00000296589(MANE Select)	SLC45A2	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000382102	SLC45A2	Deleterious	98\|2	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

5:33951588C>A_3_ENST00000509381

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Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 75|25 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:33951588C>A (GRCh38)

Gene symbol

SLC45A2

Gene constraints

LOEUF: 1.04, LOF (oe): 0.65, misssense (oe): 1.06, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000509381.1

Genbank transcript ID

NM_001297417 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.857G>T
g.33106G>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

dbSNP ID	rs16891982
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.034	1
	1.547	1
(flanking)	9.034	1

?

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

polyA signal ok

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Original cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Wildtype AA sequence

MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTDSQ GNDIKVTAES TGEHASSLPL PLHQPPHWMD SLPVQHAVLH RFHGPDCVPR
GSL*

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

62 / 62

Last intron/exon boundary

767

Theoretical NMD boundary in CDS

655

Length of CDS

732

Coding sequence (CDS) position

N/A

cDNA position

857

gDNA position

33106

Chromosomal position

33951588

Speed

0.05 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:

5:33951588C>A_1_ENST00000296589

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:33951588C>A (GRCh38)

Gene symbol

SLC45A2

Gene constraints

LOEUF: 1.02, LOF (oe): 0.78, misssense (oe): 1.02, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000296589.9

Genbank transcript ID

NM_016180 (exact from MANE)

UniProt / AlphaMissense peptide

S45A2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1122G>T
g.33106G>T

AA changes

AAE:	L374F	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs16891982
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	V	F	S	S	L	Y	S	Y
mutated	not conserved	374	Y	E	R	G	V	E	V	G	C	W	G	F	C	I	N	S	V	F	S	S	L	Y	S
Ptroglodytes	all identical	374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	V	F	S	S	L	Y	S
Mmulatta	all identical	374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	V	F	S	S	L	Y	S
Fcatus	all identical	374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	M	F	S	S	L	Y	S
Mmusculus	all identical	374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	V	F	S	S	V	Y	S
Ggallus	all identical	389	Y	R	R	G	V	E	V	G	C	W	G	L	C	I	N	A	I	A	S	S	A	Y
Trubripes	all identical	416	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	A	V	S	S	A	L	Y	S
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	430	Y	E	R	G	V	E	V	G	C	W	G	M	C	I	N	A	I	S	S	A	L	Y	S

Protein features

Start (aa)	End (aa)	Feature	Details
1	530	CHAIN		lost
367	387	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.034	1
	1.547	1
(flanking)	9.034	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

5

Strand

-1

Original gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Original cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Wildtype AA sequence

MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGLCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKERQQA PGGDPDNSVR GKGMDCATLT
CMVQLAQILV GGGLGFLVNT AGTVVVVVIT ASAVALIGCC FVALFVRYVD *

Mutated AA sequence

MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGFCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKERQQA PGGDPDNSVR GKGMDCATLT
CMVQLAQILV GGGLGFLVNT AGTVVVVVIT ASAVALIGCC FVALFVRYVD *

Position of stopcodon in wt / mu CDS

1593 / 1593

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

531 / 531

Position of stopcodon in wt / mu cDNA

1703 / 1703

Position of start ATG in wt / mu cDNA

111 / 111

Last intron/exon boundary

1478

Theoretical NMD boundary in CDS

1317

Length of CDS

1593

Coding sequence (CDS) position

1122

cDNA position

1232

gDNA position

33106

Chromosomal position

33951588

Speed

0.06 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:

5:33951588C>A_2_ENST00000382102

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:33951588C>A (GRCh38)

Gene symbol

SLC45A2

Gene constraints

LOEUF: 1.04, LOF (oe): 0.78, misssense (oe): 1.04, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000382102.7

Genbank transcript ID

NM_001012509 (by similarity)

UniProt / AlphaMissense peptide

S45A2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1122G>T
g.33106G>T

AA changes

AAE:	L374F	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs16891982
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	4	4

Protein conservation

Species	Match	AA	Alignment
Human		374	Y	E	R	G	V	E	V	G	C	W	G	L	C	I	N	S	V	F	S	S	L	Y	S	Y
mutated	not conserved	374	Y	E	R	G	V	E	V	G	C	W	G	F	C	I	N	S	V	F	S	S	L	Y	S
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	530	CHAIN		lost
367	387	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.034	1
	1.547	1
(flanking)	9.034	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

5

Strand

-1

Original gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered gDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Original cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC

Altered cDNA sequence snippet

GAGGTTGGATGTTGGGGCTTTTGCATCAACTCCGTGTTTTC

Wildtype AA sequence

MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGLCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKEVCCH *

Mutated AA sequence

MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGFCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKEVCCH *

Position of stopcodon in wt / mu CDS

1383 / 1383

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

461 / 461

Position of stopcodon in wt / mu cDNA

1441 / 1441

Position of start ATG in wt / mu cDNA

59 / 59

Last intron/exon boundary

1214

Theoretical NMD boundary in CDS

1105

Length of CDS

1383

Coding sequence (CDS) position

1122

cDNA position

1180

gDNA position

33106

Chromosomal position

33951588

Speed

0.06 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