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: ENST00000548115
Querying Taster for transcript #2: ENST00000549867
Querying Taster for transcript #3: ENST00000257915
MT speed 0.29 s - this script 2.656552 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000257915(MANE Select)	TFCP2	Deleterious	66\|34	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000548115	TFCP2	Deleterious	78\|22	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000549867	TFCP2	Benign	53\|147	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

12:51104169G>T_3_ENST00000257915

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 66|34 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:51104169G>T (GRCh38)

Gene symbol

TFCP2

Gene constraints

LOEUF: 0.56, LOF (oe): 0.39, misssense (oe): 0.58, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000257915.10

Genbank transcript ID

NM_005653 (exact from MANE), NM_001173452 (by similarity)

UniProt / AlphaMissense peptide

TFCP2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.952C>A
g.68967C>A

AA changes

AAE:	P318T	?
Score:	38

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376607235
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	15	15

Protein conservation

Species	Match	AA	Alignment
Human		318	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T	P
mutated	not conserved	318	N	G	S	P	N	H	Q	P	E	P	P	T	P	V	T	D	N	L	L	P	T	T	T
Ptroglodytes	all identical	318	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T
Mmulatta	all identical	333	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T
Fcatus	all identical	324	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T
Mmusculus	all identical	318	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T
Ggallus	all identical	318	N	G	S	P	N	H	Q	P	E	P	P	P	P	I	A	D	N	L	L	P	T	S	T
Trubripes	not conserved	361												N	P	V	LIQKMFLSPIMITADQ	Q	N	L	L	P	S	A	T
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	318	N	G	S	P	N	H	Q	P	E	P	P	A	P	I	V	DVSAGLTPIQ	N	L	L	P	T	S	T

Protein features

Start (aa)	End (aa)	Feature	Details
1	502	CHAIN		lost
133	395	REGION	DNA-binding	lost
294	325	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.697	1
	3.303	0.999
(flanking)	-0.443	0.286

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

15

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

ACCACCAGCCAGAGCCACCCCCTCCAGTCACAGATGTAAGT

Altered gDNA sequence snippet

ACCACCAGCCAGAGCCACCCACTCCAGTCACAGATGTAAGT

Original cDNA sequence snippet

ACCACCAGCCAGAGCCACCCCCTCCAGTCACAGATAACCTC

Altered cDNA sequence snippet

ACCACCAGCCAGAGCCACCCACTCCAGTCACAGATAACCTC

Wildtype AA sequence

MAWALKLPLA DEVIESGLVQ DFDASLSGIG QELGAGAYSM SDVLALPIFK QEESSLPPDN
ENKILPFQYV LCAATSPAVK LHDETLTYLN QGQSYEIRML DNRKLGELPE INGKLVKSIF
RVVFHDRRLQ YTEHQQLEGW RWNRPGDRIL DIDIPMSVGI IDPRANPTQL NTVEFLWDPA
KRTSVFIQVH CISTEFTMRK HGGEKGVPFR VQIDTFKENE NGEYTEHLHS ASCQIKVFKP
KGADRKQKTD REKMEKRTPH EKEKYQPSYE TTILTECSPW PEITYVNNSP SPGFNSSHSS
FSLGEGNGSP NHQPEPPPPV TDNLLPTTTP QEAQQWLHRN RFSTFTRLFT NFSGADLLKL
TRDDVIQICG PADGIRLFNA LKGRMVRPRL TIYVCQESLQ LREQQQQQQQ QQQKHEDGDS
NGTFFVYHAI YLEELTAVEL TEKIAQLFSI SPCQISQIYK QGPTGIHVLI SDEMIQNFQE
EACFILDTMK AETNDSYHII LK*

Mutated AA sequence

MAWALKLPLA DEVIESGLVQ DFDASLSGIG QELGAGAYSM SDVLALPIFK QEESSLPPDN
ENKILPFQYV LCAATSPAVK LHDETLTYLN QGQSYEIRML DNRKLGELPE INGKLVKSIF
RVVFHDRRLQ YTEHQQLEGW RWNRPGDRIL DIDIPMSVGI IDPRANPTQL NTVEFLWDPA
KRTSVFIQVH CISTEFTMRK HGGEKGVPFR VQIDTFKENE NGEYTEHLHS ASCQIKVFKP
KGADRKQKTD REKMEKRTPH EKEKYQPSYE TTILTECSPW PEITYVNNSP SPGFNSSHSS
FSLGEGNGSP NHQPEPPTPV TDNLLPTTTP QEAQQWLHRN RFSTFTRLFT NFSGADLLKL
TRDDVIQICG PADGIRLFNA LKGRMVRPRL TIYVCQESLQ LREQQQQQQQ QQQKHEDGDS
NGTFFVYHAI YLEELTAVEL TEKIAQLFSI SPCQISQIYK QGPTGIHVLI SDEMIQNFQE
EACFILDTMK AETNDSYHII LK*

Position of stopcodon in wt / mu CDS

1509 / 1509

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

503 / 503

Position of stopcodon in wt / mu cDNA

2222 / 2222

Position of start ATG in wt / mu cDNA

714 / 714

Last intron/exon boundary

2184

Theoretical NMD boundary in CDS

1420

Length of CDS

1509

Coding sequence (CDS) position

952

cDNA position

1665

gDNA position

68967

Chromosomal position

51104169

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

Back to summary table

MutationT@ster 2025

Variant:

12:51104169G>T_1_ENST00000548115

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 78|22 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:51104169G>T (GRCh38)

Gene symbol

TFCP2

Gene constraints

LOEUF: 0.60, LOF (oe): 0.41, misssense (oe): 0.61, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000548115.5

Genbank transcript ID

NM_001173453 (by similarity)

UniProt / AlphaMissense peptide

TFCP2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.799C>A
g.68967C>A

AA changes

AAE:	P267T	?
Score:	38

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376607235
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	15	15

Protein conservation

Species	Match	AA	Alignment
Human		267	N	G	S	P	N	H	Q	P	E	P	P	P	P	V	T	D	N	L	L	P	T	T	T	P
mutated	not conserved	267	N	G	S	P	N	H	Q	P	E	P	P	T	P	V	T	D	N	L	L	P	T	T	T
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	502	CHAIN		lost
61	300	DOMAIN	Grh/CP2 DB	lost
133	395	REGION	DNA-binding	lost
238	268	REGION		lost
239	267	COMPBIAS	Basic and acidic residues	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.697	1
	3.303	0.999
(flanking)	-0.443	0.286

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

15

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

12

Strand

-1

Original gDNA sequence snippet

ACCACCAGCCAGAGCCACCCCCTCCAGTCACAGATGTAAGT

Altered gDNA sequence snippet

ACCACCAGCCAGAGCCACCCACTCCAGTCACAGATGTAAGT

Original cDNA sequence snippet

ACCACCAGCCAGAGCCACCCCCTCCAGTCACAGATAACCTC

Altered cDNA sequence snippet

ACCACCAGCCAGAGCCACCCACTCCAGTCACAGATAACCTC

Wildtype AA sequence

MAWALKLPLA DEVIESGLVQ DFDASLSGIG QELGAGAYSM SDVLALPIFK QEESSLPPDN
ENKILPFQYV LCAATSPAVK LHDETLTYLN QGQSYEIRML DNRKLGELPE INGKLVKSIF
RVVFHDRRLQ YTEHQQLEGW RWNRPGDRIL DIDIPMSVGI IDPRANPTQL NTVEFLWDPA
KRTSVFIQPK GADRKQKTDR EKMEKRTPHE KEKYQPSYET TILTECSPWP EITYVNNSPS
PGFNSSHSSF SLGEGNGSPN HQPEPPPPVT DNLLPTTTPQ EAQQWLHRNR FSTFTRLFTN
FSGADLLKLT RDDVIQICGP ADGIRLFNAL KGRMVRPRLT IYVCQESLQL REQQQQQQQQ
QQKHEDGDSN GTFFVYHAIY LEELTAVELT EKIAQLFSIS PCQISQIYKQ GPTGIHVLIS
DEMIQNFQEE ACFILDTMKE TNDSYHIILK *

Mutated AA sequence

MAWALKLPLA DEVIESGLVQ DFDASLSGIG QELGAGAYSM SDVLALPIFK QEESSLPPDN
ENKILPFQYV LCAATSPAVK LHDETLTYLN QGQSYEIRML DNRKLGELPE INGKLVKSIF
RVVFHDRRLQ YTEHQQLEGW RWNRPGDRIL DIDIPMSVGI IDPRANPTQL NTVEFLWDPA
KRTSVFIQPK GADRKQKTDR EKMEKRTPHE KEKYQPSYET TILTECSPWP EITYVNNSPS
PGFNSSHSSF SLGEGNGSPN HQPEPPTPVT DNLLPTTTPQ EAQQWLHRNR FSTFTRLFTN
FSGADLLKLT RDDVIQICGP ADGIRLFNAL KGRMVRPRLT IYVCQESLQL REQQQQQQQQ
QQKHEDGDSN GTFFVYHAIY LEELTAVELT EKIAQLFSIS PCQISQIYKQ GPTGIHVLIS
DEMIQNFQEE ACFILDTMKE TNDSYHIILK *

Position of stopcodon in wt / mu CDS

1353 / 1353

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

451 / 451

Position of stopcodon in wt / mu cDNA

1843 / 1843

Position of start ATG in wt / mu cDNA

491 / 491

Last intron/exon boundary

1808

Theoretical NMD boundary in CDS

1267

Length of CDS

1353

Coding sequence (CDS) position

799

cDNA position

1289

gDNA position

68967

Chromosomal position

51104169

Speed

0.16 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:

12:51104169G>T_2_ENST00000549867

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 53|147 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr12:51104169G>T (GRCh38)

Gene symbol

TFCP2

Gene constraints

LOEUF: 0.57, LOF (oe): 0.38, misssense (oe): 0.54, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000549867.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.917+2356C>A
g.68967C>A

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	rs376607235
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	15	15

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.697	1
	3.303	0.999
(flanking)	-0.443	0.286

?

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

12

Strand

-1

Original gDNA sequence snippet

ACCACCAGCCAGAGCCACCCCCTCCAGTCACAGATGTAAGT

Altered gDNA sequence snippet

ACCACCAGCCAGAGCCACCCACTCCAGTCACAGATGTAAGT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAWALKLPLA DEVIESGLVQ DFDASLSGIG QELGAGAYSM SDVLALPIFK QEESSLPPDN
ENKILPFQYV LCAATSPAVK LHDETLTYLN QGQSYEIRML DNRKLGELPE INGKLVKSIF
RVVFHDRRLQ YTEHQQLEGW RWNRPGDRIL DIDIPMSVGI IDPRANPTQL NTVEFLWDPA
KRTSVFIQVH CISTEFTMRK HGGEKGVPFR VQIDTFKENE NGEYTEHLHS ASCQIKVFKP
KGADRKQKTD REKMEKRTPH EKEKYQPSYE TTILTECSPW PEITYVNNSP SPGFNSSHSS
FSLGEGMVRP RLTIYVCQES LQLREQQQQQ QQQQQKHEDG DSNGTFFVYH AIYLEELTAV
ELTEKIAQLF SISPCQISQI YKQGPTGIHV LISDEMIQNF QEEACFILDT MKAETNDSYH
IILK*

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

95 / 95

Last intron/exon boundary

1331

Theoretical NMD boundary in CDS

1186

Length of CDS

1275

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

68967

Chromosomal position

51104169

Speed

0.01 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