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: ENST00000264867
Querying Taster for transcript #2: ENST00000613098
MT speed 0.03 s - this script 2.412686 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
ENST00000264867(MANE Select)	PPARGC1A	Benign	3\|197	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000613098	PPARGC1A	Benign	4\|196	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

4:23817261C>T_1_ENST00000264867

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 3|197 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr4:23817261C>T (GRCh38)

Gene symbol

PPARGC1A

Gene constraints

LOEUF: 0.38, LOF (oe): 0.27, misssense (oe): 0.87, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000264867.7

Genbank transcript ID

NM_013261 (exact from MANE), NM_001354827 (by similarity), NM_001354825 (by similarity), NM_001330752 (by similarity), NM_001330751 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.878-2656G>A
g.86829G>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	rs2932971
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	5404	28160	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.355	1
	1.179	1
(flanking)	1.935	1

?

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

4

Strand

-1

Original gDNA sequence snippet

AGTTATTTAAGCGATAATGAGCTTGGGTACTAGGACAAGGG

Altered gDNA sequence snippet

AGTTATTTAAGCGATAATGAACTTGGGTACTAGGACAAGGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAWDMCNQDS ESVWSDIECA ALVGEDQPLC PDLPELDLSE LDVNDLDTDS FLGGLKWCSD
QSEIISNQYN NEPSNIFEKI DEENEANLLA VLTETLDSLP VDEDGLPSFD ALTDGDVTTD
NEASPSSMPD GTPPPQEAEE PSLLKKLLLA PANTQLSYNE CSGLSTQNHA NHNHRIRTNP
AIVKTENSWS NKAKSICQQQ KPQRRPCSEL LKYLTTNDDP PHTKPTENRN SSRDKCTSKK
KSHTQSQSQH LQAKPTTLSL PLTPESPNDP KGSPFENKTI ERTLSVELSG TAGLTPPTTP
PHKANQDNPF RASPKLKSSC KTVVPPPSKK PRYSESSGTQ GNNSTKKGPE QSELYAQLSK
SSVLTGGHEE RKTKRPSLRL FGDHDYCQSI NSKTEILINI SQELQDSRQL ENKDVSSDWQ
GQICSSTDSD QCYLRETLEA SKQVSPCSTR KQLQDQEIRA ELNKHFGHPS QAVFDDEADK
TGELRDSDFS NEQFSKLPMF INSGLAMDGL FDDSEDESDK LSYPWDGTQS YSLFNVSPSC
SSFNSPCRDS VSPPKSLFSQ RPQRMRSRSR SFSRHRSCSR SPYSRSRSRS PGSRSSSRSC
YYYESSHYRH RTHRNSPLYV RSRSRSPYSR RPRYDSYEEY QHERLKREEY RREYEKRESE
RAKQRERQRQ KAIEERRVIY VGKIRPDTTR TELRDRFEVF GEIEECTVNL RDDGDSYGFI
TYRYTCDAFA ALENGYTLRR SNETDFELYF CGRKQFFKSN YADLDSNSDD FDPASTKSKY
DSLDFDSLLK EAQRSLRR*

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

91 / 91

Last intron/exon boundary

2383

Theoretical NMD boundary in CDS

2242

Length of CDS

2397

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

86829

Chromosomal position

23817261

Speed

0.02 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:

4:23817261C>T_2_ENST00000613098

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 4|196 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr4:23817261C>T (GRCh38)

Gene symbol

PPARGC1A

Gene constraints

LOEUF: 0.43, LOF (oe): 0.31, misssense (oe): 0.88, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000613098.4

Genbank transcript ID

NM_001354826 (by similarity), NM_001330753 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.497-2656G>A
g.86829G>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	rs2932971
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	5404	28160	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.355	1
	1.179	1
(flanking)	1.935	1

?

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

4

Strand

-1

Original gDNA sequence snippet

AGTTATTTAAGCGATAATGAGCTTGGGTACTAGGACAAGGG

Altered gDNA sequence snippet

AGTTATTTAAGCGATAATGAACTTGGGTACTAGGACAAGGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MPDGTPPPQE AEEPSLLKKL LLAPANTQLS YNECSGLSTQ NHANHNHRIR TNPAIVKTEN
SWSNKAKSIC QQQKPQRRPC SELLKYLTTN DDPPHTKPTE NRNSSRDKCT SKKKSHTQSQ
SQHLQAKPTT LSLPLTPESP NDPKGSPFEN KTIERTLSVE LSGTAGLTPP TTPPHKANQD
NPFRASPKLK SSCKTVVPPP SKKPRYSESS GTQGNNSTKK GPEQSELYAQ LSKSSVLTGG
HEERKTKRPS LRLFGDHDYC QSINSKTEIL INISQELQDS RQLENKDVSS DWQGQICSST
DSDQCYLRET LEASKQVSPC STRKQLQDQE IRAELNKHFG HPSQAVFDDE ADKTGELRDS
DFSNEQFSKL PMFINSGLAM DGLFDDSEDE SDKLSYPWDG TQSYSLFNVS PSCSSFNSPC
RDSVSPPKSL FSQRPQRMRS RSRSFSRHRS CSRSPYSRSR SRSPGSRSSS RSCYYYESSH
YRHRTHRNSP LYVRSRSRSP YSRRPRYDSY EEYQHERLKR EEYRREYEKR ESERAKQRER
QRQKAIEERR VIYVGKIRPD TTRTELRDRF EVFGEIEECT VNLRDDGDSY GFITYRYTCD
AFAALENGYT LRRSNETDFE LYFCGRKQFF KSNYADLDSN SDDFDPASTK SKYDSLDFDS
LLKEAQRSLR R*

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

712 / 712

Last intron/exon boundary

2623

Theoretical NMD boundary in CDS

1861

Length of CDS

2016

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

86829

Chromosomal position

23817261

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