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: ENST00000372088
Querying Taster for transcript #2: ENST00000359979
Querying Taster for transcript #3: ENST00000224756
MT speed 0.17 s - this script 2.579348 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
ENST00000359979	CCSER2	Deleterious	83\|17	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000224756	CCSER2	Deleterious	83\|17	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000372088(MANE Select)	CCSER2	Benign	42\|58	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

10:84372068A>C_2_ENST00000359979

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 83|17 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84372068A>C (GRCh38)

Gene symbol

CCSER2

Gene constraints

LOEUF: 0.63, LOF (oe): 0.40, misssense (oe): 0.93, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000359979.8

Genbank transcript ID

NM_001284241 (by similarity)

UniProt / AlphaMissense peptide

CCSE2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1016A>C
g.43483A>C

AA changes

AAE:	N339T	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs771179017
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	7	7

Protein conservation

Species	Match	AA	Alignment
Human		339	S	P	F	S	G	T	M	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E	D
mutated	not conserved	339	S	P	F	S	G	T	M	T	V	D	G	T	K	N	S	P	A	D	T	C	V	E	E
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	834	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.759	1
	2.269	1
(flanking)	1.664	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

10

Strand

1

Original gDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered gDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

Original cDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered cDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

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 ESSEMNSIVC
MDLYTLGIFC LPYYRETCDM IDFVKNL*

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 SGTMTVDGTK NSPADTCVEE DATVLAKDRA
ANKDQELIEN ESYRTKNNQT MKHDAKMRYL SDDVDDISLS SLSSSDKNDL SEDFSDDFID
IEDSNRTRIT PEEMSLKEEK HENGPPQDMF DSPKENEKAF SKTDEWIDIS VSDRSECTKH
TSGNNLVSPD TDYRAGSSFE LSPSDSSDGT YMWDEEGLEP IGNVHPVGSY ESSEMNSIVC
MDLYTLGIFC LPYYRETCDM IDFVKNL*

Position of stopcodon in wt / mu CDS

1704 / 1704

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

568 / 568

Position of stopcodon in wt / mu cDNA

1966 / 1966

Position of start ATG in wt / mu cDNA

263 / 263

Last intron/exon boundary

1679

Theoretical NMD boundary in CDS

1366

Length of CDS

1704

Coding sequence (CDS) position

1016

cDNA position

1278

gDNA position

43483

Chromosomal position

84372068

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

Back to summary table

MutationT@ster 2025

Variant:

10:84372068A>C_3_ENST00000224756

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 83|17 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84372068A>C (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

CCSE2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1016A>C
g.43483A>C

AA changes

AAE:	N339T	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs771179017
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	7	7

Protein conservation

Species	Match	AA	Alignment
Human		339	S	P	F	S	G	T	M	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E	D
mutated	not conserved	339	S	P	F	S	G	T	M	T	V	D	G	T	K	N	S	P	A	D	T	C	V	E	E
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	834	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.759	1
	2.269	1
(flanking)	1.664	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

10

Strand

1

Original gDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered gDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

Original cDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered cDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

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

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 SGTMTVDGTK 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*

Position of stopcodon in wt / mu CDS

2505 / 2505

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

835 / 835

Position of stopcodon in wt / mu cDNA

2690 / 2690

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

1016

cDNA position

1201

gDNA position

43483

Chromosomal position

84372068

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

Back to summary table

MutationT@ster 2025

Variant:

10:84372068A>C_1_ENST00000372088

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 42|58 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:84372068A>C (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.1016A>C
g.43483A>C

AA changes

AAE:	N339T	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs771179017
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	7	7

Protein conservation

Species	Match	AA	Alignment
Human		339	S	P	F	S	G	T	M	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E	D
mutated	not conserved	339	S	P	F	S	G	T	M	T	V	D	G	T	K	N	S	P	A	D	T	C	V	E	E
Ptroglodytes	all identical	339	S	P	F	S	G	T	M	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E
Mmulatta	all identical	339	S	P	F	S	G	T	I	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E
Fcatus	all identical	339	P	P	F	S	G	T	I	T	V	D	G	N	K	N	S	P	A	D	T	C	V	E	E
Mmusculus	all identical	338	P	P	F	S	G	P	M	T	V	D	S	N	K	N	P	P	A	D	M	C	V	E	E
Ggallus	not conserved	337	Q	R	F	A	G	N	I	I	M	D	G	G	K	S	T	T	P	D	T	Y	I	V	E
Trubripes	not conserved	250	K	PL	F	F	G	R	-	-	V	K	G	T	G	P	S	A	V	S	E	CGTPSA	V
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	331	S	H	L	A	M	D	L	I	T	D	S	T	K	M	S	S	H	I	S	S	V	T	E

Protein features

Start (aa)	End (aa)	Feature	Details
1	834	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.759	1
	2.269	1
(flanking)	1.664	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

10

Strand

1

Original gDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered gDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

Original cDNA sequence snippet

GACTATGACAGTTGATGGAAATAAAAATTCACCTGCTGACA

Altered cDNA sequence snippet

GACTATGACAGTTGATGGAACTAAAAATTCACCTGCTGACA

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 SGTMTVDGTK 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*

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

1016

cDNA position

1275

gDNA position

43483

Chromosomal position

84372068

Speed

0.07 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