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: ENST00000296255
Querying Taster for transcript #2: ENST00000497289
MT speed 0.08 s - this script 2.512353 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
ENST00000497289	RPN1	Deleterious	79\|21	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed
ENST00000296255(MANE Select)	RPN1	Deleterious	84\|16	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

3:128625917G>T_2_ENST00000497289

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 79|21 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:128625917G>T (GRCh38)

Gene symbol

RPN1

Gene constraints

LOEUF: 0.30, LOF (oe): 0.15, misssense (oe): 0.82, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000497289.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.716C>A
g.55159C>A

AA changes

AAE:	A239D	?
Score:	126

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs761651988
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	10	10

Protein conservation

Species	Match	AA	Alignment
Human		239	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q	H	I	Q	D
mutated	not conserved	239	Y	L	D	T	F	G	R	P	V	I	V	D	Y	K	K	N	L	V	E	Q	H	I	Q
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.071	0.978
	9.336	1
(flanking)	7.364	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

3

Strand

-1

Original gDNA sequence snippet

TGGCCGCCCTGTGATTGTTGCCTACAAGAAAAATCTGGTAG

Altered gDNA sequence snippet

TGGCCGCCCTGTGATTGTTGACTACAAGAAAAATCTGGTAG

Original cDNA sequence snippet

TGGCCGCCCTGTGATTGTTGCCTACAAGAAAAATCTGGTAG

Altered cDNA sequence snippet

TGGCCGCCCTGTGATTGTTGACTACAAGAAAAATCTGGTAG

Wildtype AA sequence

MRVKLASRNV ESYTKLGNPT RSEDLLDYGP FRDVPAYSQD TFKVHYENNS PFLTITSMTR
VIEVSHWGNI AVEENVDLKH TGAVLKGPFS RYDYQRQPDS GISSIRSFKT ILPAAAQDVY
YRDEIGNVST SHLLILDDSV EMEIRPRFPL FGGWKTHYIV GYNLPSYEYL YNLGDQYALK
MRFVDHVFDE QVIDSLTVKI ILPEGAKNIE IDSPYEISRA PDELHYTYLD TFGRPVIVAY
KKNLVEQHIQ DIVVHYTFNK VLMLQEPLLV VAAFYILFFT VIIYVRLDFS ITKDPAAEAR
MKVACITEQV LTLVNKRIGL YRHFDETVNR YKQSRDISTL NSGKKSLETE HKALTSEIAL
LQSRLKTEGS DLCDRVSEMQ KLDAQVKELV LKSAVEAERL VAGKLKKDTY IENEKLISGK
RQELVTKIDH ILDAL*

Mutated AA sequence

MRVKLASRNV ESYTKLGNPT RSEDLLDYGP FRDVPAYSQD TFKVHYENNS PFLTITSMTR
VIEVSHWGNI AVEENVDLKH TGAVLKGPFS RYDYQRQPDS GISSIRSFKT ILPAAAQDVY
YRDEIGNVST SHLLILDDSV EMEIRPRFPL FGGWKTHYIV GYNLPSYEYL YNLGDQYALK
MRFVDHVFDE QVIDSLTVKI ILPEGAKNIE IDSPYEISRA PDELHYTYLD TFGRPVIVDY
KKNLVEQHIQ DIVVHYTFNK VLMLQEPLLV VAAFYILFFT VIIYVRLDFS ITKDPAAEAR
MKVACITEQV LTLVNKRIGL YRHFDETVNR YKQSRDISTL NSGKKSLETE HKALTSEIAL
LQSRLKTEGS DLCDRVSEMQ KLDAQVKELV LKSAVEAERL VAGKLKKDTY IENEKLISGK
RQELVTKIDH ILDAL*

Position of stopcodon in wt / mu CDS

1308 / 1308

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

436 / 436

Position of stopcodon in wt / mu cDNA

1885 / 1885

Position of start ATG in wt / mu cDNA

578 / 578

Last intron/exon boundary

1702

Theoretical NMD boundary in CDS

1074

Length of CDS

1308

Coding sequence (CDS) position

716

cDNA position

1293

gDNA position

55159

Chromosomal position

128625917

Speed

0.03 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:

3:128625917G>T_1_ENST00000296255

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 84|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:128625917G>T (GRCh38)

Gene symbol

RPN1

Gene constraints

LOEUF: 0.30, LOF (oe): 0.17, misssense (oe): 0.89, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000296255.8

Genbank transcript ID

NM_002950 (exact from MANE)

UniProt / AlphaMissense peptide

RPN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1232C>A
g.55159C>A

AA changes

AAE:	A411D	?
Score:	126

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs761651988
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	10	10

Protein conservation

Species	Match	AA	Alignment
Human		411	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q	H	I	Q	D
mutated	not conserved	411	Y	L	D	T	F	G	R	P	V	I	V	D	Y	K	K	N	L	V	E	Q	H
Ptroglodytes	all identical	411	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q	H
Mmulatta	all identical	411	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q	H
Fcatus	all identical	411	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q	H
Mmusculus	all identical	412	Y	L	D	T	F	G	R	P	V	I	V	A	Y	K	K	N	L	V	E	Q
Ggallus	all identical	496	Y	L	D	T	F	G	R	P	V	I	V	A	H	K	N	N	L	V	E	Q	H	I	Q
Trubripes	all identical	407	Y	L	D	T	F	G	R	P	V	L	V	A	T	K	N	N	L	V	E	H	H	I	Q
Drerio	no homologue
Dmelanogaster	not conserved	399	Y	L	D	T	I	G	R	P	V	V	S	F	S	K	S	N	L	V	E	S	H	I	S
Celegans	not conserved	394	Y	L	D	T	T	G	R	L	V	L	V	L	E	K	E	N	I	V	P	D	H	S	Q
Xtropicalis	all identical	408	Y	L	D	T	F	G	R	T	V	I	V	A	H	K	N	N	L	V	E	Q	H	I

Protein features

Start (aa)	End (aa)	Feature	Details
24	438	TOPO_DOM	Lumenal	lost
24	607	CHAIN		lost
406	413	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.071	0.978
	9.336	1
(flanking)	7.364	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

3

Strand

-1

Original gDNA sequence snippet

TGGCCGCCCTGTGATTGTTGCCTACAAGAAAAATCTGGTAG

Altered gDNA sequence snippet

TGGCCGCCCTGTGATTGTTGACTACAAGAAAAATCTGGTAG

Original cDNA sequence snippet

TGGCCGCCCTGTGATTGTTGCCTACAAGAAAAATCTGGTAG

Altered cDNA sequence snippet

TGGCCGCCCTGTGATTGTTGACTACAAGAAAAATCTGGTAG

Wildtype AA sequence

MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG
GSTSRATSFL LALEPELEAR LAHLGVQVKG EDEEENNLEV RETKIKGKSG RFFTVKLPVA
LDPGAKISVI VETVYTHVLH PYPTQITQSE KQFVVFEGNH YFYSPYPTKT QTMRVKLASR
NVESYTKLGN PTRSEDLLDY GPFRDVPAYS QDTFKVHYEN NSPFLTITSM TRVIEVSHWG
NIAVEENVDL KHTGAVLKGP FSRYDYQRQP DSGISSIRSF KTILPAAAQD VYYRDEIGNV
STSHLLILDD SVEMEIRPRF PLFGGWKTHY IVGYNLPSYE YLYNLGDQYA LKMRFVDHVF
DEQVIDSLTV KIILPEGAKN IEIDSPYEIS RAPDELHYTY LDTFGRPVIV AYKKNLVEQH
IQDIVVHYTF NKVLMLQEPL LVVAAFYILF FTVIIYVRLD FSITKDPAAE ARMKVACITE
QVLTLVNKRI GLYRHFDETV NRYKQSRDIS TLNSGKKSLE TEHKALTSEI ALLQSRLKTE
GSDLCDRVSE MQKLDAQVKE LVLKSAVEAE RLVAGKLKKD TYIENEKLIS GKRQELVTKI
DHILDAL*

Mutated AA sequence

MEAPAAGLFL LLLLGTWAPA PGSASSEAPP LINEDVKRTV DLSSHLAKVT AEVVLAHLGG
GSTSRATSFL LALEPELEAR LAHLGVQVKG EDEEENNLEV RETKIKGKSG RFFTVKLPVA
LDPGAKISVI VETVYTHVLH PYPTQITQSE KQFVVFEGNH YFYSPYPTKT QTMRVKLASR
NVESYTKLGN PTRSEDLLDY GPFRDVPAYS QDTFKVHYEN NSPFLTITSM TRVIEVSHWG
NIAVEENVDL KHTGAVLKGP FSRYDYQRQP DSGISSIRSF KTILPAAAQD VYYRDEIGNV
STSHLLILDD SVEMEIRPRF PLFGGWKTHY IVGYNLPSYE YLYNLGDQYA LKMRFVDHVF
DEQVIDSLTV KIILPEGAKN IEIDSPYEIS RAPDELHYTY LDTFGRPVIV DYKKNLVEQH
IQDIVVHYTF NKVLMLQEPL LVVAAFYILF FTVIIYVRLD FSITKDPAAE ARMKVACITE
QVLTLVNKRI GLYRHFDETV NRYKQSRDIS TLNSGKKSLE TEHKALTSEI ALLQSRLKTE
GSDLCDRVSE MQKLDAQVKE LVLKSAVEAE RLVAGKLKKD TYIENEKLIS GKRQELVTKI
DHILDAL*

Position of stopcodon in wt / mu CDS

1824 / 1824

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

608 / 608

Position of stopcodon in wt / mu cDNA

1842 / 1842

Position of start ATG in wt / mu cDNA

19 / 19

Last intron/exon boundary

1659

Theoretical NMD boundary in CDS

1590

Length of CDS

1824

Coding sequence (CDS) position

1232

cDNA position

1250

gDNA position

55159

Chromosomal position

128625917

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