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: ENST00000543283
Querying Taster for transcript #2: ENST00000372088
Querying Taster for transcript #3: ENST00000224756
MT speed 0.18 s - this script 2.594357 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
ENST00000224756	CCSER2	Benign	1\|99	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000543283	CCSER2	Benign	2\|98	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000372088(MANE Select)	CCSER2	Benign	48\|52	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD

MutationT@ster 2025

Variant:

10:84513849C>T_3_ENST00000224756

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84513849C>T (GRCh38)

Gene symbol

CCSER2

Gene constraints

LOEUF: 0.62, LOF (oe): 0.43, misssense (oe): 0.95, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000224756.12

Genbank transcript ID

NM_001351290 (by similarity), NM_001351292 (by similarity), NM_018999 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2996C>T
g.185264C>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	rs117675200
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7	3292	3299

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.966	0.05
	-0.252	0
(flanking)	-0.624	0

?

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

10

Strand

1

Original gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Original cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Wildtype AA sequence

MEEKTQIKTF LGSKLPKYGT KSVRSTLQPM PNGTPVNLLG TSKNSNVKSY IKNNGSDCPS
SHSFNWRKAN KYQLCAQGVE EPNNTQNSHD KIIDPEKRVP TQGMFDKNGI KGGLKSVSLF
TSKLAKPSTM FVSSTEELNQ KSFSGPSNLG KFTKGTLLGR TSYSSINTPK SQLNGFYGNR
SAGSMQRPRA NSCATRSSSG ESLAQSPDSS KSINCEKMVR SQSFSHSIQN SFLPPSSITR
SHSFNRAVDL TKPYQNQQLS IRVPLRSSML TRNSRQPEVL NGNEHLGYGF NRPYAAGGKK
LALPNGPGVT STLGYRMVHP SLLKSSRSPF SGTMTVDGNK NSPADTCVEE DATVLAKDRA
ANKDQELIEN ESYRTKNNQT MKHDAKMRYL SDDVDDISLS SLSSSDKNDL SEDFSDDFID
IEDSNRTRIT PEEMSLKEEK HENGPPQDMF DSPKENEKAF SKTDEWIDIS VSDRSECTKH
TSGNNLVSPD TDYRAGSSFE LSPSDSSDGT YMWDEEGLEP IGNVHPVGSY ESSEMNSIDI
LNNLESCDLE DDDLMLDVDL PEDAPLENVE CDNMNRFDRP DRNVRQPQEG FWKRPPQRWS
GQEHYHLSHP DHYHHHGKSD LSRGSPYRES PLGHFESYGG MPFFQAQKMF VDVPENTVIL
DEMTLRHMVQ DCTAVKTQLL KLKRLLHQHD GSGSLHDIQL SLPSSPEPED GDKVYKNEDL
LNEIKQLKDE IKKKDEKIQL LELQLATQHI CHQKCKEEKC TYADKYTQTP WRRIPGGYSA
PSFSPWQGSF QGIPRTVPPH RRQTSSTTAF QQPSQTHRSH PGKTNKATTY RGPQ*

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

186 / 186

Last intron/exon boundary

2595

Theoretical NMD boundary in CDS

2359

Length of CDS

2505

Coding sequence (CDS) position

N/A

cDNA position

2996

gDNA position

185264

Chromosomal position

84513849

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

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MutationT@ster 2025

Variant:

10:84513849C>T_1_ENST00000543283

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 2|98 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84513849C>T (GRCh38)

Gene symbol

CCSER2

Gene constraints

LOEUF: 0.96, LOF (oe): 0.53, misssense (oe): 1.04, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000543283.2

Genbank transcript ID

NM_001284243 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1216C>T
g.185264C>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	rs117675200
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7	3292	3299

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.966	0.05
	-0.252	0
(flanking)	-0.624	0

?

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

10

Strand

1

Original gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Original cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Wildtype AA sequence

MNRFDRPDRN VRQPQEGFWK RPPQRWSGQE HYHLSHPDHY HHHGKSDLSR GSPYRESPLG
HFESYGGMPF FQAQKMFVDV PENTVILDEM TLRHMVQDCT AVKTQLLKLK RLLHQHDGSG
SLHDIQLSLP SSPEPEDGDK VYKNEDLLNE IKQLKDEIKK KDEKIQLLEL QLATQHICHQ
KCKEEKCTYA DKYTQTPWRR IPGGYSAPSF SPWQGSFQGI PRTVPPHRRQ TSSTTAFQQP
SQTHRSHPGK TNKATTYRGP Q*

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

125 / 125

Last intron/exon boundary

815

Theoretical NMD boundary in CDS

640

Length of CDS

786

Coding sequence (CDS) position

N/A

cDNA position

1216

gDNA position

185264

Chromosomal position

84513849

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:

10:84513849C>T_2_ENST00000372088

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 48|52 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84513849C>T (GRCh38)

Gene symbol

CCSER2

Gene constraints

LOEUF: 0.59, LOF (oe): 0.43, misssense (oe): 0.94, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000372088.8

Genbank transcript ID

NM_001284240 (exact from MANE)

UniProt / AlphaMissense peptide

CCSE2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2726C>T
g.185264C>T

AA changes

AAE:	P909L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs117675200
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	7	3292	3299

Protein conservation

Species	Match	AA	Alignment
Human		909	D	Q	A	K	R	V	G	R	N	Q	S	P	P	V	G	Y	M	S	Q	P	K	S	L	Q
mutated	not conserved	909				K	R	V	G	R	N	Q	S	L	P	V	G	Y	M	S	Q	P	K	S	L
Ptroglodytes	not conserved	909				K	R	V	G	R	N	Q	S	L	P	V	G	Y	M	S	Q	P	K	S	L
Mmulatta	all identical	909				K	R	V	G	R	N	Q	S	P	P	V	G	Y	V	S	Q	P	K	S	L
Fcatus	not conserved	906				T	R	V	G	R	N	Q	S	S	L	E	G	Y	T	S	Q	P	K	S	L
Mmusculus	all identical	908				K	R	G	G	R	N	Q	C	P	-	-	-	-	-	-	Q	P	K	S	L
Ggallus	all identical	915	E	V	R	T	E	V	A	V	K	G	Q	P	S	F	T	Y	QA	S	R	P	K	T	S
Trubripes	all identical	49											S	P	K	V	G	S	K	M	G	P	S	S	M
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	941	S	R	S	V	T	K	P	T	S	S	S	L	P	-	G	Q	I	P	R	P	T	T	L

Protein features

No protein features affected

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.966	0.05
	-0.252	0
(flanking)	-0.624	0

?

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

10

Strand

1

Original gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered gDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Original cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCCGCCAGTGGGTTATATGTCTC

Altered cDNA sequence snippet

AGTTGGAAGAAATCAGTCTCTGCCAGTGGGTTATATGTCTC

Wildtype AA sequence

MEEKTQIKTF LGSKLPKYGT KSVRSTLQPM PNGTPVNLLG TSKNSNVKSY IKNNGSDCPS
SHSFNWRKAN KYQLCAQGVE EPNNTQNSHD KIIDPEKRVP TQGMFDKNGI KGGLKSVSLF
TSKLAKPSTM FVSSTEELNQ KSFSGPSNLG KFTKGTLLGR TSYSSINTPK SQLNGFYGNR
SAGSMQRPRA NSCATRSSSG ESLAQSPDSS KSINCEKMVR SQSFSHSIQN SFLPPSSITR
SHSFNRAVDL TKPYQNQQLS IRVPLRSSML TRNSRQPEVL NGNEHLGYGF NRPYAAGGKK
LALPNGPGVT STLGYRMVHP SLLKSSRSPF SGTMTVDGNK NSPADTCVEE DATVLAKDRA
ANKDQELIEN ESYRTKNNQT MKHDAKMRYL SDDVDDISLS SLSSSDKNDL SEDFSDDFID
IEDSNRTRIT PEEMSLKEEK HENGPPQDMF DSPKENEKAF SKTDEWIDIS VSDRSECTKH
TSGNNLVSPD TDYRAGSSFE LSPSDSSDGT YMWDEEGLEP IGNVHPVGSY ESSEMNSIDI
LNNLESCDLE DDDLMLDVDL PEDAPLENVE CDNMNRFDRP DRNVRQPQEG FWKRPPQRWS
GQEHYHLSHP DHYHHHGKSD LSRGSPYRES PLGHFESYGG MPFFQAQKMF VDVPENTVIL
DEMTLRHMVQ DCTAVKTQLL KLKRLLHQHD GSGSLHDIQL SLPSSPEPED GDKVYKNEDL
LNEIKQLKDE IKKKDEKIQL LELQLATQHI CHQKCKEEKC TYADKYTQTP WRRIPPQVLQ
PSSSLPRPTD HTQGKLIKPQ RIEARSECSI QDMHQGGAHP EESFTHVLHQ ESNYGLEEQP
FSSGPQLTMD VAKSTPSEAN LNITVNAQEP YHLANNQISD MQFIPTSLQT PPESSTVDQA
KRVGRNQSPP VGYMSQPKSL QLLKPSILSS LVPPPVSESS PSRTPTCKKS PIITTCNSAK
LQPTSSQTNL ANNQNLKASK LRPPSGSFKQ KQTNSPQLEP QSFQAKTSIP RPLTQRKEIM
QNPNGNLHSG DCLASNRYSR LPKPKIH*

Mutated AA sequence

MEEKTQIKTF LGSKLPKYGT KSVRSTLQPM PNGTPVNLLG TSKNSNVKSY IKNNGSDCPS
SHSFNWRKAN KYQLCAQGVE EPNNTQNSHD KIIDPEKRVP TQGMFDKNGI KGGLKSVSLF
TSKLAKPSTM FVSSTEELNQ KSFSGPSNLG KFTKGTLLGR TSYSSINTPK SQLNGFYGNR
SAGSMQRPRA NSCATRSSSG ESLAQSPDSS KSINCEKMVR SQSFSHSIQN SFLPPSSITR
SHSFNRAVDL TKPYQNQQLS IRVPLRSSML TRNSRQPEVL NGNEHLGYGF NRPYAAGGKK
LALPNGPGVT STLGYRMVHP SLLKSSRSPF SGTMTVDGNK NSPADTCVEE DATVLAKDRA
ANKDQELIEN ESYRTKNNQT MKHDAKMRYL SDDVDDISLS SLSSSDKNDL SEDFSDDFID
IEDSNRTRIT PEEMSLKEEK HENGPPQDMF DSPKENEKAF SKTDEWIDIS VSDRSECTKH
TSGNNLVSPD TDYRAGSSFE LSPSDSSDGT YMWDEEGLEP IGNVHPVGSY ESSEMNSIDI
LNNLESCDLE DDDLMLDVDL PEDAPLENVE CDNMNRFDRP DRNVRQPQEG FWKRPPQRWS
GQEHYHLSHP DHYHHHGKSD LSRGSPYRES PLGHFESYGG MPFFQAQKMF VDVPENTVIL
DEMTLRHMVQ DCTAVKTQLL KLKRLLHQHD GSGSLHDIQL SLPSSPEPED GDKVYKNEDL
LNEIKQLKDE IKKKDEKIQL LELQLATQHI CHQKCKEEKC TYADKYTQTP WRRIPPQVLQ
PSSSLPRPTD HTQGKLIKPQ RIEARSECSI QDMHQGGAHP EESFTHVLHQ ESNYGLEEQP
FSSGPQLTMD VAKSTPSEAN LNITVNAQEP YHLANNQISD MQFIPTSLQT PPESSTVDQA
KRVGRNQSLP VGYMSQPKSL QLLKPSILSS LVPPPVSESS PSRTPTCKKS PIITTCNSAK
LQPTSSQTNL ANNQNLKASK LRPPSGSFKQ KQTNSPQLEP QSFQAKTSIP RPLTQRKEIM
QNPNGNLHSG DCLASNRYSR LPKPKIH*

Position of stopcodon in wt / mu CDS

3144 / 3144

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

1048 / 1048

Position of stopcodon in wt / mu cDNA

3403 / 3403

Position of start ATG in wt / mu cDNA

260 / 260

Last intron/exon boundary

2584

Theoretical NMD boundary in CDS

2274

Length of CDS

3144

Coding sequence (CDS) position

2726

cDNA position

2985

gDNA position

185264

Chromosomal position

84513849

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