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: ENST00000391993
Querying Taster for transcript #2: ENST00000373327
MT speed 0.21 s - this script 2.656986 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000373327(MANE Select)	TRAF3IP1	Benign	25\|75	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000391993	TRAF3IP1	Benign	30\|70	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

2:238397627A>C_2_ENST00000373327

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 25|75 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:238397627A>C (GRCh38)

Gene symbol

TRAF3IP1

Gene constraints

LOEUF: 0.72, LOF (oe): 0.57, misssense (oe): 0.94, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000373327.5

Genbank transcript ID

NM_015650 (exact from MANE)

UniProt / AlphaMissense peptide

MIPT3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1858A>C
g.77187A>C

AA changes

AAE:	M620L	?
Score:	15

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3739070
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	5344	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		620	E	D	V	D	A	M	Q	N	E	L	Q	M	W	H	S	E	N	R	Q	H	A	E	A	L
mutated	all conserved	620	E	D	V	D	A	M	Q	N	E	L	Q	L	W	H	S	E	N	R	Q	H	A	E	A
Ptroglodytes	all conserved	620	E	D	V	D	A	M	Q	N	E	L	Q	L	W	H	S	E	N	R	Q	H	A	E	A
Mmulatta	all conserved	619	E	D	V	D	A	M	Q	N	E	L	Q	L	W	H	S	E	N	R	Q	H	A	E	A
Fcatus	all conserved	650										L	Q	L	W	H	S	E	N	K	Q	H	A	E	A
Mmusculus	all conserved	583	E	D	V	D	A	M	Q	N	E	L	Q	L	W	H	S	E	N	R	Q	H	A	E	A
Ggallus	all identical	620	E	D	M	D	A	M	K	N	E	L	Q	M	W	R	H	E	N	R	Q	H	A	E	A
Trubripes	not conserved	579	E	N	I	D	A	M	Q	A	E	L	I	F	L	R	Q	E	S	K	K	Y	M	Q	A
Drerio	no homologue
Dmelanogaster	all identical	523	E	D	F	D	A	M	Q	L	E	L	T	M	W	R	D	T	Y	T	Q	A	S	T	E
Celegans	not conserved	470	D	D	I	E	S	M	I	K	E	L	E	R	W	R	S	E	Q	R	R	N	E	Q	E
Xtropicalis	all identical	561	E	D	V	D	T	M	Q	N	E	L	Q	M	W	R	R	E	N	N	Q	H	A	K	A

Protein features

Start (aa)	End (aa)	Feature
1	691	CHAIN	lost
223	691	REGION	lost
571	666	COILED	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.087	1
	0.126	0.958
(flanking)	1.15	0.992

?

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

2

Strand

1

Original gDNA sequence snippet

CCATGCAGAATGAGCTGCAGATGTGGCACAGCGAGAACAGG

Altered gDNA sequence snippet

CCATGCAGAATGAGCTGCAGCTGTGGCACAGCGAGAACAGG

Original cDNA sequence snippet

CCATGCAGAATGAGCTGCAGATGTGGCACAGCGAGAACAGG

Altered cDNA sequence snippet

CCATGCAGAATGAGCTGCAGCTGTGGCACAGCGAGAACAGG

Wildtype AA sequence

MNAAVVRRTQ EALGKVIRRP PLTEKLLSKP PFRYLHDIIT EVIRMTGFMK GLYTDAEMKS
DNVKDKDAKI SFLQKAIDVV VMVSGEPLLA KPARIVAGHE PERTNELLQI IGKCCLNKLS
SDDAVRRVLA GEKGEVKGRA SLTSRSQELD NKNVREEESR VHKNTEDRGD AEIKERSTSR
DRKQKEELKE DRKPREKDKD KEKAKENGGN RHREGERERA KARARPDNER QKDRGNRERD
RDSERKKETE RKSEGGKEKE RLRDRDRERD RDKGKDRDRR RVKNGEHSWD LDREKNREHD
KPEKKSASSG EMSKKLSDGT FKDSKAETET EISTRASKSL TTKTSKRRSK NSVEGRKEDN
ISAKSLDSIV SGINNEPNQE TTTSEIGTKE ANINSTSISD DNSASLRCEN IQPNPTEKQK
GDSTSDAEGD AGPAGQDKSE VPETPEIPNE LSSNIRRIPR PGSARPAPPR VKRQDSMEAL
QMDRSGSGKT VSNVITESHN SDNEEDDQFV VEAAPQLSEM SEIEMVTAVE LEEEEKHGGL
VKKILETKKD YEKLQQSPKP GEKERSLFES AWKKEKDIVS KEIEKLRTSI QTLCKSALPL
GKIMDYIQED VDAMQNELQM WHSENRQHAE ALQQEQRITD CAVEPLKAEL AELEQLIKDQ
QDKICAVKAN ILKNEEKIQK MVYSINLTSR R*

Mutated AA sequence

MNAAVVRRTQ EALGKVIRRP PLTEKLLSKP PFRYLHDIIT EVIRMTGFMK GLYTDAEMKS
DNVKDKDAKI SFLQKAIDVV VMVSGEPLLA KPARIVAGHE PERTNELLQI IGKCCLNKLS
SDDAVRRVLA GEKGEVKGRA SLTSRSQELD NKNVREEESR VHKNTEDRGD AEIKERSTSR
DRKQKEELKE DRKPREKDKD KEKAKENGGN RHREGERERA KARARPDNER QKDRGNRERD
RDSERKKETE RKSEGGKEKE RLRDRDRERD RDKGKDRDRR RVKNGEHSWD LDREKNREHD
KPEKKSASSG EMSKKLSDGT FKDSKAETET EISTRASKSL TTKTSKRRSK NSVEGRKEDN
ISAKSLDSIV SGINNEPNQE TTTSEIGTKE ANINSTSISD DNSASLRCEN IQPNPTEKQK
GDSTSDAEGD AGPAGQDKSE VPETPEIPNE LSSNIRRIPR PGSARPAPPR VKRQDSMEAL
QMDRSGSGKT VSNVITESHN SDNEEDDQFV VEAAPQLSEM SEIEMVTAVE LEEEEKHGGL
VKKILETKKD YEKLQQSPKP GEKERSLFES AWKKEKDIVS KEIEKLRTSI QTLCKSALPL
GKIMDYIQED VDAMQNELQL WHSENRQHAE ALQQEQRITD CAVEPLKAEL AELEQLIKDQ
QDKICAVKAN ILKNEEKIQK MVYSINLTSR R*

Position of stopcodon in wt / mu CDS

2076 / 2076

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

692 / 692

Position of stopcodon in wt / mu cDNA

2221 / 2221

Position of start ATG in wt / mu cDNA

146 / 146

Last intron/exon boundary

2055

Theoretical NMD boundary in CDS

1859

Length of CDS

2076

Coding sequence (CDS) position

1858

cDNA position

2003

gDNA position

77187

Chromosomal position

238397627

Speed

0.10 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:

2:238397627A>C_1_ENST00000391993

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 30|70 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:238397627A>C (GRCh38)

Gene symbol

TRAF3IP1

Gene constraints

LOEUF: 0.68, LOF (oe): 0.53, misssense (oe): 0.93, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000391993.7

Genbank transcript ID

NM_001139490 (by similarity)

UniProt / AlphaMissense peptide

MIPT3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1660A>C
g.77187A>C

AA changes

AAE:	M554L	?
Score:	15

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3739070
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	5344	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		554	E	D	V	D	A	M	Q	N	E	L	Q	M	W	H	S	E	N	R	Q	H	A	E	A	L
mutated	all conserved	554	E	D	V	D	A	M	Q	N	E	L	Q	L	W	H	S	E	N	R	Q	H	A	E	A
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	691	CHAIN		lost
223	691	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.087	1
	0.126	0.958
(flanking)	1.15	0.992

?

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

2

Strand

1

Original gDNA sequence snippet

CCATGCAGAATGAGCTGCAGATGTGGCACAGCGAGAACAGG

Altered gDNA sequence snippet

CCATGCAGAATGAGCTGCAGCTGTGGCACAGCGAGAACAGG

Original cDNA sequence snippet

CCATGCAGAATGAGCTGCAGATGTGGCACAGCGAGAACAGG

Altered cDNA sequence snippet

CCATGCAGAATGAGCTGCAGCTGTGGCACAGCGAGAACAGG

Wildtype AA sequence

MNAAVVRRTQ EALGKVIRRP PLTEKLLSKP PFRYLHDIIT EVIRMTGFMK GLYTDAEMKS
DNVKDKDAKI SFLQKAIDVV VMVSGEPLLA KPARIVAGHE PERTNELLQI IGKCCLNKLS
SDDAVRRVLA GEKGEVKGRA SLTSRSQELD NKNVREEESR VHKNTEDRGD AEIKERSTSR
DRKQKEELKE DRKPREKDKD KEKAKENGGN RHREGERERA KARARPDNER QKDRGNRERD
RDSERKKETE RKSEGGKEKE RLRDRDRERD RDKGKDRDRR RVKNGEHSWD LDREKNREHD
KPEKKSASSG EMSKKLSDGT FKDSKAETET EISTRASKSL TTKTSKRRSK NSVEGDSTSD
AEGDAGPAGQ DKSEVPETPE IPNELSSNIR RIPRPGSARP APPRVKRQDS MEALQMDRSG
SGKTVSNVIT ESHNSDNEED DQFVVEAAPQ LSEMSEIEMV TAVELEEEEK HGGLVKKILE
TKKDYEKLQQ SPKPGEKERS LFESAWKKEK DIVSKEIEKL RTSIQTLCKS ALPLGKIMDY
IQEDVDAMQN ELQMWHSENR QHAEALQQEQ RITDCAVEPL KAELAELEQL IKDQQDKICA
VKANILKNEE KIQKMVYSIN LTSRR*

Mutated AA sequence

MNAAVVRRTQ EALGKVIRRP PLTEKLLSKP PFRYLHDIIT EVIRMTGFMK GLYTDAEMKS
DNVKDKDAKI SFLQKAIDVV VMVSGEPLLA KPARIVAGHE PERTNELLQI IGKCCLNKLS
SDDAVRRVLA GEKGEVKGRA SLTSRSQELD NKNVREEESR VHKNTEDRGD AEIKERSTSR
DRKQKEELKE DRKPREKDKD KEKAKENGGN RHREGERERA KARARPDNER QKDRGNRERD
RDSERKKETE RKSEGGKEKE RLRDRDRERD RDKGKDRDRR RVKNGEHSWD LDREKNREHD
KPEKKSASSG EMSKKLSDGT FKDSKAETET EISTRASKSL TTKTSKRRSK NSVEGDSTSD
AEGDAGPAGQ DKSEVPETPE IPNELSSNIR RIPRPGSARP APPRVKRQDS MEALQMDRSG
SGKTVSNVIT ESHNSDNEED DQFVVEAAPQ LSEMSEIEMV TAVELEEEEK HGGLVKKILE
TKKDYEKLQQ SPKPGEKERS LFESAWKKEK DIVSKEIEKL RTSIQTLCKS ALPLGKIMDY
IQEDVDAMQN ELQLWHSENR QHAEALQQEQ RITDCAVEPL KAELAELEQL IKDQQDKICA
VKANILKNEE KIQKMVYSIN LTSRR*

Position of stopcodon in wt / mu CDS

1878 / 1878

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

626 / 626

Position of stopcodon in wt / mu cDNA

2100 / 2100

Position of start ATG in wt / mu cDNA

223 / 223

Last intron/exon boundary

1934

Theoretical NMD boundary in CDS

1661

Length of CDS

1878

Coding sequence (CDS) position

1660

cDNA position

1882

gDNA position

77187

Chromosomal position

238397627

Speed

0.11 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