MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.86, LOF (oe): 0.76, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000684235.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WEDSLKDGHQ LKQLLLKALT LMLDAAESYA
KDSCVRQAQH CQRLTKLITL QIHFLNTGQN TMLINLGRHK LMDCILALPR FYQASIVAEA
YDFVPDWAEI LYQQVILKGD FNYLEEFKQQ RLLKSSIFEE ISKKILHFYL TH*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

7179 / 4848

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

2393 / 1616

Position of stopcodon in wt / mu cDNA

7210 / 4879

Position of start ATG in wt / mu cDNA

32 / 32

Last intron/exon boundary

7182

Theoretical NMD boundary in CDS

7100

Length of CDS

7179

Coding sequence (CDS) position

4846

cDNA position

4877

gDNA position

74377

Chromosomal position

44589312

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

MutationT@ster 2025

Variant:

15:44589312G>A_2_ENST00000682065

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.85, LOF (oe): 0.75, misssense (oe): 1.04, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000682065.1

Genbank transcript ID

NM_001411132 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEAHV ACEHPTGWSS MEERHLLLTL AGHWLAQEDV
VPLDKLEELE KQIWLCRITQ HTLGRNQEET EPRFSRQIST SGELSFDSLA SEFSFSKLAA
LNTSKYLELN SLPSKETCEN RLDWKEQESL NFLIGRLLDD GCVHEASRVC RYFHFYNPDV
ALVLHCRALA SGEASMEDLH PEIHALLQSA ELLEEEAPDI PLRRVHSTSS LDSQKFVTVP
SSNEVVTNLE VLTSKCLHGK NYCRQVLCLY DLAKELGCSY TDVAAQDGEA MLRKILASQQ
PDRCKRAQAF ISTQGLKPDT VAELVAEEVT RELLTSSQGT GHKQMFNPTE ESQTFLQLTT
LCQDRTLVGM KLLDKISSVP HGELSCTTEL LILAHHCFTL TCHMEGIIRV LQAAHMLTDN
HLAPSEEYGL VVRLLTGIGR YNEMTYIFDL LHKKHYFEVL MRKKLDPSGT LKTALLDYIK
RCRPGDSEKH NMIALCFSMC REIGENHEAA ARIQLKLIES QPWEDSLKDG HQLKQLLLKA
LTLMLDAAES YAKDSCVRQA QHCQRLTKLI TLQIHFLNTG QNTMLINLGR HKLMDCILAL
PRFYQASIVA EAYDFVPDWA EILYQQVILK GDFNYLEEFK QQRLLKSSIF EEISKKYKQH
QPTDMVMENL KKLLTYCEDV YLYYKLAYEH KFYEIVNVLL KDPQTGCCLK DMLAG*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

7188 / 4848

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

2396 / 1616

Position of stopcodon in wt / mu cDNA

7219 / 4879

Position of start ATG in wt / mu cDNA

32 / 32

Last intron/exon boundary

7038

Theoretical NMD boundary in CDS

6956

Length of CDS

7188

Coding sequence (CDS) position

4846

cDNA position

4877

gDNA position

74377

Chromosomal position

44589312

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

MutationT@ster 2025

Variant:

15:44589312G>A_3_ENST00000682669

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.87, LOF (oe): 0.77, misssense (oe): 1.03, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000682669.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4645C>T
g.74377C>T

AA changes

Q1549* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1549	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QELIKSKTPK QLIQQVGNEA YVIGLSSFHI PSIGAACVCF LELLGLDSLK
LRVDMKVANI ILSYKCRNED AQYSFIRESV AEKLSKLADG EKTTTEELLV LLEEGTWNSI
QQQEIKRLSS ESSSQWALVV QFCRLHNMKL SISYLRECAK ANDWLQFIIH SQLHNYHPAE
VKSLIQYFSP VIQDHLRLAF ENLPSVPTSK MDSDQVCNKC PQELQGSKQE MTDLFEILLQ
CSEEPDSWHW LLVEAVKQQA PILSVLASCL QGASAISCLC VWIITSVEDN VATEAMGHIQ
DSTEDHTWNL EDLSVIWRTL LTRQKSKTLI RGFQLFFKDS PLLLVMEMYE LCMFFRNYKE
AEAKLLEFQK SLETLNTAAT KVHPVIPAMW LEDQVCFLLK LMLQQCKTQY ELGKLLQLFV
EREHLFSDGP DVKKLCILCQ ILKDTSIAIN HTIITSYSIE NLQHECRSIL ERLQTDGQFA
LARRVAELAE LPVDNLVIKE ITQEMQTLKH IEQWSLKQAR IDFWKKCHEN FKKNSISSKA
ASSFFSTQAH VACEHPTGWS SMEERHLLLT LAGHWLAQED VVPLDKLEEL EKQIWLCRIT
QHTLGRNQEE TEPRFSRQIS TSGELSFDSL ASEFSFSKLA ALNTSKYLEL NSLPSKETCE
NRLDWKEQES LNFLIGRLLD DGCVHEASRV CRYFHFYNPD VALVLHCRAL ASGEASMEDL
HPEIHALLQS AELLEEEAPD IPLRRVHSTS SLDSQKFVTV PSSNEVVTNL EVLTSKCLHG
KNYCRQVLCL YDLAKELGCS YTDVAAQDGE AMLRKILASQ QPDRCKRAQA FISTQGLKPD
TVAELVAEEV TRELLTSSQG TGHKQMFNPT EESQTFLQLT TLCQDRTLVG MKLLDKISSV
PHGELSCTTE LLILAHHCFT LTCHMEGIIR VLQAAHMLTD NHLAPSEEYG LVVRLLTGIG
RYNEMTYIFD LLHKKHYFEV LMRKKLDPSG TLKTALLDYI KRCRPGDSEK HNMIALCFSM
CREIGENHEA AARIQLKLIE SQPWEDSLKD GHQLKQLLLK ALTLMLDAAE SYAKDSCVRQ
AQHCQRLTKL ITLQIHFLNT GQNTMLINLG RHKLMDCILA LPRFYQASIV AEAYDFVPDW
AEILYQQVIL KGDFNYLEEF KQQRLLKSSI FEEISKKYKQ HQPTDMVMEN LKKLLTYCED
VYLYYKLAYE HKFYEIVNVL LKDPQTGCCL KDMLAG*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QELIKSKTPK QLIQQVGNEA YVIGLSSFHI PSIGAACVCF LELLGLDSLK
LRVDMKVANI ILSYKCRNED AQYSFIRESV AEKLSKLADG EKTTTEELLV LLEEGTWNSI
QQQEIKRLSS ESSSQWALVV QFCRLHNMKL SISYLRECAK ANDWLQFIIH SQLHNYHPAE
VKSLIQYFSP VIQDHLRLAF ENLPSVPTSK MDSDQVCNKC PQELQGSKQE MTDLFEILLQ
CSEEPDSWHW LLVEAVKQQA PILSVLASCL QGASAISCLC VWIITSVEDN VATEAMGHIQ
DSTEDHTWNL EDLSVIWRTL LTRQKSKTLI RGFQLFFKDS PLLLVMEMYE LCMFFRNYKE
AEAKLLEFQK SLETLNTAAT KVHPVIPAMW LEDQVCFLLK LMLQQCKT*

Position of stopcodon in wt / mu CDS

7131 / 4647

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

2377 / 1549

Position of stopcodon in wt / mu cDNA

7162 / 4678

Position of start ATG in wt / mu cDNA

32 / 32

Last intron/exon boundary

6981

Theoretical NMD boundary in CDS

6899

Length of CDS

7131

Coding sequence (CDS) position

4645

cDNA position

4676

gDNA position

74377

Chromosomal position

44589312

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

MutationT@ster 2025

Variant:

15:44589312G>A_4_ENST00000427534

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.84, LOF (oe): 0.74, misssense (oe): 1.03, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000427534.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1614	C	F	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V
mutated	all conserved	1614	C	F	L	L	K	L	M	L	Q	Q	C	K	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WDINNISLLT WSWKT*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

6798 / 4848

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

2266 / 1616

Position of stopcodon in wt / mu cDNA

6798 / 4848

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

6754

Theoretical NMD boundary in CDS

6703

Length of CDS

6798

Coding sequence (CDS) position

4846

cDNA position

4846

gDNA position

74377

Chromosomal position

44589312

Speed

0.09 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

MutationT@ster 2025

Variant:

15:44589312G>A_5_ENST00000558319

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.84, LOF (oe): 0.74, misssense (oe): 1.02, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000558319.5

Genbank transcript ID

UniProt / AlphaMissense peptide

SPTCS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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	2443	CHAIN		lost
1955	1955	MOD_RES	Phosphoserine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGA LPPGDSQPL*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

6240 / 4848

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

2080 / 1616

Position of stopcodon in wt / mu cDNA

6271 / 4879

Position of start ATG in wt / mu cDNA

32 / 32

Last intron/exon boundary

6037

Theoretical NMD boundary in CDS

5955

Length of CDS

6240

Coding sequence (CDS) position

4846

cDNA position

4877

gDNA position

74377

Chromosomal position

44589312

Speed

0.08 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

MutationT@ster 2025

Variant:

15:44589312G>A_6_ENST00000535302

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.87, LOF (oe): 0.77, misssense (oe): 1.04, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000535302.6

Genbank transcript ID

NM_001160227 (by similarity)

UniProt / AlphaMissense peptide

SPTCS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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	2443	CHAIN		lost
1955	1955	MOD_RES	Phosphoserine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSRHKQM FNPTEESQTF LQLTTLCQDR
TLVGMKLLDK ISSVPHGELS CTTELLILAH HCFTLTCHME GIIRVLQAAH MLTDNHLAPS
EEYGLVVRLL TGIGRYNEMT YIFDLLHKKH YFEVLMRKKL DPSGTLKTAL LDYIKRCRPG
DSEKHNMIAL CFSMCREIGE NHEAAARIQL KLIESQPWED SLKDGHQLKQ LLLKALTLML
DAAESYAKDS CVRQAQHCQR LTKLITLQIH FLNTGQNTML INLGRHKLMD CILALPRFYQ
ASIVAEAYDF VPDWAEILYQ QVILKGDFNY LEEFKQQRLL KSSIFEEISK KYKQHQPTDM
VMENLKKLLT YCEDVYLYYK LAYEHKFYEI VNVLLKDPQT GCCLKDMLAG *

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

6993 / 4848

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

2331 / 1616

Position of stopcodon in wt / mu cDNA

7021 / 4876

Position of start ATG in wt / mu cDNA

29 / 29

Last intron/exon boundary

6840

Theoretical NMD boundary in CDS

6761

Length of CDS

6993

Coding sequence (CDS) position

4846

cDNA position

4874

gDNA position

74377

Chromosomal position

44589312

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

MutationT@ster 2025

Variant:

15:44589312G>A_8_ENST00000559511

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.86, LOF (oe): 0.77, misssense (oe): 1.03, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000559511.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E
mutated	no alignment	n/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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTTELL ILAHHCFTLT CHMEGIIRVL
QAAHMLTDNH LAPSEEYGLV VRLLTGIGRY NEMTYIFDLL HKKHYFEVLM RKKLDPSGTL
KTALLDYIKR CRPGDSEKHN MIALCFSMCR EIGENHEAAA RIQLKLIESQ PWEDSLKDGH
QLKQLLLKAL TLMLDAAESY AKDSCVRQAQ HCQRLTKLIT LQIHFLNTGQ NTMLINLGRH
KLMDCILALP RFYQASIVAE AYDFVPDWAE ILYQQVILKG DFNYLEEFKQ QRLLKSSIFE
EISKKYKQHQ PTDMVMENLK KLLTYCEDVY LYYKLAYEHK FYEIVNVLLK DPQTGCCLKD
MLAG*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

6855 / 4848

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

2285 / 1616

Position of stopcodon in wt / mu cDNA

6855 / 4848

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

6674

Theoretical NMD boundary in CDS

6623

Length of CDS

6855

Coding sequence (CDS) position

4846

cDNA position

4846

gDNA position

74377

Chromosomal position

44589312

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

MutationT@ster 2025

Variant:

15:44589312G>A_7_ENST00000261866

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 41319 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:44589312G>A (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.85, LOF (oe): 0.76, misssense (oe): 1.03, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000261866.12

Genbank transcript ID

NM_025137 (exact from MANE)

UniProt / AlphaMissense peptide

SPTCS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4846C>T
g.74377C>T

AA changes

Q1616* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hereditary spastic paraplegia 11

pathogenic

Variant DBs

dbSNP ID	rs312262762
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E	R	E	H	L	F	S	D	G	P	D	V	K	K	L	C	I	L	C	Q	I	L	K	D	T	S	I	A	I	N	H	T	I	I	T	S	Y	S	I	E	N	L	Q	H	E	C	R	S	I	L	E	R	L	Q	T	D	G	Q	F	A	L	A	R	R	V	A	E	L	A	E	L	P	V	D	N	L	V	I	K	E	I	T	Q	E	M	Q	T	L	K	H	I	E	Q	W	S	L	K	Q	A	R
mutated	no alignment	n/a
Ptroglodytes	partly conserved	1616	L	L	K	L	M	L	Q	Q	C	K	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	E	R	E	H	L	F	S	D	V	P	D	V	K	K	L	C	V	L	C	Q	I	L	K	D	T	S	I	A	I	N	H	T	I	I	T	S	Y	S	I	E	N	L	Q	H	E	C	R	S	I	L	E	R	L
Mmulatta	partly conserved	1661	L	L	K	L	M	L	Q	Q	C	K	T	P	Y	E	L	G	K	L	L	Q	L	F	V	E	R	E	H	L	F	S	D	G	P	D	V	K	K	L	Y	V	L	C	Q	I	L	K	D	T	S	I	A	I	N	H	I	I	I	T	C	Y	S	I	E	N	F	Q	H	E	C	K	S	I	L	E	R	L
Fcatus	partly conserved	1615	L	L	K	L	M	L	Q	Q	C	G	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	G	I	E	H	L	F	C	D	G	P	D	V	K	K	L	C	V	L	S	K	I	L	K	D	T	S	I	A	I	N	P	V	V	I	S	S	Y	S	P	E	N	F	Q	H	E	C	R	S	I	L	E	K	L
Mmusculus	partly conserved	1602	L	L	K	L	M	P	Q	Q	C	E	T	Q	Y	E	L	G	K	L	L	Q	L	F	V	G	T	E	Q	L	F	S	D	G	P	D	V	Q	K	L	C	L	L	S	Q	V	L	K	D	T	P	I	A	I	S	P	A	V	I	S	S	Y	S	T	E	N	F	Q	R	E	C	R	S	I	L	E	K	L
Ggallus	partly conserved	1598	L	L	E	L	M	M	Q	Q	C	R	T	E	Y	E	L	G	K	L	L	Q	L	F	A	A	T	D	N	L	L	L	D	G	P	Y	V	K	K	L	C	A	L	S	E	T	L	R	D	S	S	V	P	I	N	R	S	M	L	T	R	Y	T	P	E	T	F	Q	K	E	C	T	S	I	L	E	Q	L	Q	E	K	G
Trubripes	partly conserved	1557	L	L	L	S	M	L	Q	R	C	S	S	Q	F	D	L	H	R	L	L	Q	L	L	A	D	V	D	K	L	LK	S	N	G	L	D	F	R	K	L	S	Q	L	S	Q	L	L	Q	D	S	D	V	S	L	S	P	R	L	L	Q	C	I	S	A	S	V	Q	Q	E	E	F	Q	A	I	V	E	A	L	Q	A	R	G	R	Y	S	Q	A	R	Q	V	A	Q	L	A	G	L	S	I	Q
Drerio	no homologue
Dmelanogaster	partly conserved	917	-	-	G	L	L	L	I	Q	L	Q	S	N	F	D	C	I	L	Q	Q	Q	R	F	L	E	C	I	-	C	R	S	D	V	G	D	I	C	D	L	L	D	F	C	L	L	H	K	V	F	G	V	A	A	T	W	L	R	E	L	S	I	D	L	E	Q	L	G	R	R	D	S	P	E	Y	K	R	L	V	D	A	L	T	E	A	R	A	Y	E	E	A	L	Q	L	A	T	L	L	Q	L	P	L	T	D	I	V	Y	G	K	W	M	T	E
Celegans	no homologue
Xtropicalis	partly conserved	1541	L	L	Q	L	L	L	L	Q	T	Q	T	P	Y	E	L	R	K	V	L	Q	L	L	S	D	K	AKP	Q	L	F	G	-	G	I	D	V	H	K	L	S	D	L	T	S	I	L	Q	D	H	P	I	A	I	S	K	E	L	I	C	H	Y	S	P	E	A	L	Q	V	E	C	Q	R	L	I	Q	M	L	L	D	K	R	I	F	S	L	A	Q	R	V	A	E	L	A	E	L	P	T	D	S	I	V	I	E	E	V	L	Q	D	Q	C	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	2443	CHAIN		lost
1955	1955	MOD_RES	Phosphoserine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.401	1
	4.398	1
(flanking)	-0.117	0.954

?

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

15

Strand

-1

Original gDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered gDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Original cDNA sequence snippet

TGCTACAGCAGTGTAAGACCCAGTATGAGCTGGGGAAGCTT

Altered cDNA sequence snippet

TGCTACAGCAGTGTAAGACCTAGTATGAGCTGGGGAAGCTT

Wildtype AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKTQYELG
KLLQLFVERE HLFSDGPDVK KLCILCQILK DTSIAINHTI ITSYSIENLQ HECRSILERL
QTDGQFALAR RVAELAELPV DNLVIKEITQ EMQTLKHIEQ WSLKQARIDF WKKCHENFKK
NSISSKAASS FFSTQAHVAC EHPTGWSSME ERHLLLTLAG HWLAQEDVVP LDKLEELEKQ
IWLCRITQHT LGRNQEETEP RFSRQISTSG ELSFDSLASE FSFSKLAALN TSKYLELNSL
PSKETCENRL DWKEQESLNF LIGRLLDDGC VHEASRVCRY FHFYNPDVAL VLHCRALASG
EASMEDLHPE IHALLQSAEL LEEEAPDIPL RRVHSTSSLD SQKFVTVPSS NEVVTNLEVL
TSKCLHGKNY CRQVLCLYDL AKELGCSYTD VAAQDGEAML RKILASQQPD RCKRAQAFIS
TQGLKPDTVA ELVAEEVTRE LLTSSQGTGH KQMFNPTEES QTFLQLTTLC QDRTLVGMKL
LDKISSVPHG ELSCTTELLI LAHHCFTLTC HMEGIIRVLQ AAHMLTDNHL APSEEYGLVV
RLLTGIGRYN EMTYIFDLLH KKHYFEVLMR KKLDPSGTLK TALLDYIKRC RPGDSEKHNM
IALCFSMCRE IGENHEAAAR IQLKLIESQP WEDSLKDGHQ LKQLLLKALT LMLDAAESYA
KDSCVRQAQH CQRLTKLITL QIHFLNTGQN TMLINLGRHK LMDCILALPR FYQASIVAEA
YDFVPDWAEI LYQQVILKGD FNYLEEFKQQ RLLKSSIFEE ISKKYKQHQP TDMVMENLKK
LLTYCEDVYL YYKLAYEHKF YEIVNVLLKD PQTGCCLKDM LAG*

Mutated AA sequence

MAAEEGVASA ASAGGSWGTA AMGRVLPMLL VPVPAEAMGQ LGSRAQLRTQ PEALGSLTAA
GSLQVLSLTP GSRGGGRCCL EGPFWHFLWE DSRNSSTPTE KPKLLALGEN YELLIYEFNL
KDGRCDATIL YSCSREALQK LIDDQDISIS LLSLRILSFH NNTSLLFINK CVILHIIFPE
RDAAIRVLNC FTLPLPAQAV DMIIDTQLCR GILFVLSSLG WIYIFDVVDG TYVAHVDLAL
HKEDMCNEQQ QEPAKISSFT SLKVSQDLDV AVIVSSSNSA VALNLNLYFR QHPGHLLCER
ILEDLPIQGP KGVDEDDPVN SAYNMKLAKF SFQIDRSWKA QLSSLNETIK NSKLEVSCCA
PWFQDILHLE SPESGNHSTS VQSWAFIPQD IMHGQYNVLQ KDHAKTSDPG RSWKIMHISE
QEEPIELKCV SVTGFTALFT WEVERMGYTI TLWDLETQGM QCFSLGTKCI PVDSSGDQQL
CFVLTENGLS LILFGLTQEE FLNRLMIHGS ASTVDTLCHL NGWGRCSIPI HALEAGIENR
QLDTVNFFLK SKENLFNPSS KSSVSDQFDH LSSHLYLRNV EELIPALDLL CSAIRESYSE
PQSKHFSEQL LNLTLSFLNN QIKELFIHTE ELDEHLQKGV NILTSYINEL RTFMIKFPWK
LTDAIDEYDV HENVPKVKES NIWKKLSFEE VIASAILNNK IPEAQTFFRI DSHSAQKLEE
LIGIGLNLVF DNLKKNNIKE ASELLKNMGF DVKGQLLKIC FYTTNKNIRD FLVEILKEKN
YFSEKEKRTI DFVHQVEKLY LGHFQENMQI QSFPRYWIKE QDFFKHKSVL DSFLKYDCKD
EFNKQDHRIV LNWALWWDQL TQESILLPRI SPEEYKSYSP EALWRYLTAR HDWLNIILWI
GEFQTQHSYA SLQQNKWPLL TVDVINQNTS CNNYMRNEIL DKLARNGVFL ASELEDFECF
LLRLSRIGGV IQDTLPVQNY KTKEGWDFHS QFILYCLEHS LQHLLYVYLD CYKLSPENCP
FLEKKELHEA HPWFEFLVQC RQVASNLTDP KLIFQASLAN AQILIPTNQA SVSSMLLEGH
TLLALATTMY SPGGVSQVVQ NEENENCLKK VDPQLLKMAL TPYPKLKTAL FPQCTPPSVL
PSDITIYHLI QSLSPFDPSR LFGWQSANTL AIGDAWSHLP HFSSPDLVNK YAIVERLNFA
YYLHNGRPSF AFGTFLVQEL IKSKTPKQLI QQVGNEAYVI GLSSFHIPSI GAACVCFLEL
LGLDSLKLRV DMKVANIILS YKCRNEDAQY SFIRESVAEK LSKLADGEKT TTEELLVLLE
EGTWNSIQQQ EIKRLSSESS SQWALVVQFC RLHNMKLSIS YLRECAKAND WLQFIIHSQL
HNYHPAEVKS LIQYFSPVIQ DHLRLAFENL PSVPTSKMDS DQVCNKCPQE LQGSKQEMTD
LFEILLQCSE EPDSWHWLLV EAVKQQAPIL SVLASCLQGA SAISCLCVWI ITSVEDNVAT
EAMGHIQDST EDHTWNLEDL SVIWRTLLTR QKSKTLIRGF QLFFKDSPLL LVMEMYELCM
FFRNYKEAEA KLLEFQKSLE TLNTAATKVH PVIPAMWLED QVCFLLKLML QQCKT*

Position of stopcodon in wt / mu CDS

7332 / 4848

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

2444 / 1616

Position of stopcodon in wt / mu cDNA

7347 / 4863

Position of start ATG in wt / mu cDNA

16 / 16

Last intron/exon boundary

7166

Theoretical NMD boundary in CDS

7100

Length of CDS

7332

Coding sequence (CDS) position

4846

cDNA position

4861

gDNA position

74377

Chromosomal position

44589312

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