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: ENST00000424347
Querying Taster for transcript #2: ENST00000645398
Querying Taster for transcript #3: ENST00000643347
Querying Taster for transcript #4: ENST00000647199
Querying Taster for transcript #5: ENST00000643499
Querying Taster for transcript #6: ENST00000643273
Querying Taster for transcript #7: ENST00000415759
Querying Taster for transcript #8: ENST00000376597
Querying Taster for transcript #9: ENST00000277082
Querying Taster for transcript #10: ENST00000642669
Querying Taster for transcript #11: ENST00000642214
Querying Taster for transcript #12: ENST00000643847
Querying Taster for transcript #13: ENST00000376598
MT speed 0.18 s - this script 2.703507 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000643347	CEP78	Deleterious	184\|16	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000376597	CEP78	Deleterious	184\|16	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000277082	CEP78	Deleterious	184\|16	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000642214	CEP78	Deleterious	184\|16	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000424347	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000645398	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000647199	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000643499	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000643273(MANE Select)	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000415759	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000642669	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000643847	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost
ENST00000376598	CEP78	Deleterious	185\|15	without_aae	No	Single base exchange	N/A	Heterozygous in gnomAD Splice site lost

MutationT@ster 2025

Variant:

9:78266441G>C_3_ENST00000643347

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 184|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.55, LOF (oe): 1.18, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000643347.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1816-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVIWR
HRGLATKKPV SSGRKHSLGK EYYAPAPLPP GVSGFLPWRT AERAKRHRGF PLIKTRDICN
QLQQPGFPVT VTVESPSSSE VEEVDDSSES VHEVPEKTSI EQEALQEKLE ECLKQLKEER
VIRLKVDKRV SELEHENAQL RNINFSLSEA LHAQSLTNMI LDDEGVLGSI ENSFQKFHAF
LDLLKDAGLG QLATMAGIDQ SDFQLLGHPQ MTSTVSNPPK EEKKALEDEK PEPKQNALGQ
MQNIQFQKIT GDARIPLPLD SFPVPVSTPE GLGTSSNNLG VPATEQRQES FEGFIARMCS
PSPDATSGTG SQRKEEELSR NSRSSSEKKT KTGEYTKKHS DKQHPGKDLH S*

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

280 / 280

Last intron/exon boundary

2094

Theoretical NMD boundary in CDS

1764

Length of CDS

2136

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

Back to summary table

MutationT@ster 2025

Variant:

9:78266441G>C_8_ENST00000376597

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 184|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.54, LOF (oe): 1.17, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000376597.9

Genbank transcript ID

NM_001098802 (by similarity)

UniProt / AlphaMissense peptide

CEP78_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1849-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVGLA
TKKPVSSGRK HSLGKEYYAP APLPPGVSGF LPWRTAERAK RHRGFPLIKT RDICNQLQQP
GFPVTVTVES PSSSEVEEVD DSSESVHEVP EKTSIEQEAL QEKLEECLKQ LKEERVIRLK
VDKRVSELEH ENAQLRNINF SLSEALHAQS LTNMILDDEG VLGSIENSFQ KFHAFLDLLK
DAGLGQLATM AGIDQSDFQL LGHPQMTSTV SNPPKEEKKA LEDEKPEPKQ NALGQMQNIQ
VSICMQSAYN EGTLMKFQKI TGDARIPLPL DSFPVPVSTP EGLGTSSNNL GVPATEQRQE
SFEGFIARMC SPSPDATSGT GSQRKEEELS RNSRSSSEKK TKTGEYTKKH SDKQHPGKDL
HS*

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

145 / 145

Last intron/exon boundary

1992

Theoretical NMD boundary in CDS

1797

Length of CDS

2169

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

Back to summary table

MutationT@ster 2025

Variant:

9:78266441G>C_9_ENST00000277082

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 184|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.55, LOF (oe): 1.18, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000277082.9

Genbank transcript ID

NM_001330694 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1798-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIGLAT
KKPVSSGRKH SLGKEYYAPA PLPPGVSGFL PWRTAERAKR HRGFPLIKTR DICNQLQQPG
FPVTVTVESP SSSEVEEVDD SSESVHEVPE KTSIEQEALQ EKLEECLKQL KEERVIRLKV
DKRVSELEHE NAQLRNINFS LSEALHAQSL TNMILDDEGV LGSIENSFQK FHAFLDLLKD
AGLGQLATMA GIDQSDFQLL GHPQMTSTVS NPPKEEKKAL EDEKPEPKQN ALGQMQNIQF
QKITGDARIP LPLDSFPVPV STPEGLGTSS NNLGVPATEQ RQESFEGFIA RMCSPSPDAT
SGTGSQRKEE ELSRNSRSSS EKKTKTGEYT KKHSDKQHPG KDLHS*

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

120 / 120

Last intron/exon boundary

1916

Theoretical NMD boundary in CDS

1746

Length of CDS

2118

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_11_ENST00000642214

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 184|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.55, LOF (oe): 1.18, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000642214.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1738-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVIWR
HRGLATKKPV SSGRKHSLGK EYYAPAPLPP GVSGFLPWRT AERAKRHRGF PLIKTRDICN
QLQQPGFPVT VTVESPSSSE VEEVDDSSES VHEVPEKTSI EQEALQLEHE NAQLRNINFS
LSEALHAQSL TNMILDDEGV LGSIENSFQK FHAFLDLLKD AGLGQLATMA GIDQSDFQLL
GHPQMTSTVS NPPKEEKKAL EDEKPEPKQN ALGQMQNIQF QKITGDARIP LPLDSFPVPV
STPEGLGTSS NNLGVPATEQ RQESFEGFIA RMCSPSPDAT SGTGSQRKEE ELSRNSRSSS
EKKTKTGEYT KKHSDKQHPG KDLHS*

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

55 / 55

Last intron/exon boundary

1791

Theoretical NMD boundary in CDS

1686

Length of CDS

2058

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_1_ENST00000424347

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.53, LOF (oe): 1.19, misssense (oe): 1.12, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000424347.6

Genbank transcript ID

NM_001349840 (by similarity), NM_001330693 (by similarity)

UniProt / AlphaMissense peptide

CEP78_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1798-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIGLAT
KKPVSSGRKH SLGKEYYAPA PLPPGVSGFL PWRTAERAKR HRGFPLIKTR DICNQLQQPG
FPVTVTVESP SSSEVEEVDD SSESVHEVPE KTSIEQEALQ EKLEECLKQL KEERVIRLKV
DKRVSELEHE NAQLRNINFS LSEALHAQSL TNMILDDEGV LGSIENSFQK FHAFLDLLKD
AGLGQLATMA GIDQSDFQLL GHPQMTSTVS NPPKEEKKAL EDEKPEPKQN ALGQMQNIQF
QKITGDARIP LPLDSFPVPV STPEGLGTSS NNLGVPATEQ RQESFEGFIA RMCSPSPDAT
SGTGSQRKEE ELSRNSRSSS EKKTKTESH*

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

290 / 290

Last intron/exon boundary

2348

Theoretical NMD boundary in CDS

2008

Length of CDS

2070

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

Back to summary table

MutationT@ster 2025

Variant:

9:78266441G>C_2_ENST00000645398

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.58, LOF (oe): 1.21, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000645398.1

Genbank transcript ID

NM_001349838 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1846-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIGLAT
KKPVSSGRKH SLGKEYYAPA PLPPGVSGFL PWRTAERAKR HRGFPLIKTR DICNQLQQPG
FPVTVTVESP SSSEVEEVDD SSESVHEVPE KTSIEQEALQ EKLEECLKQL KEERVIRLKV
DKRVSELEHE NAQLRNINFS LSEALHAQSL TNMILDDEGV LGSIENSFQK FHAFLDLLKD
AGLGQLATMA GIDQSDFQLL GHPQMTSTVS NPPKEEKKAL EDEKPEPKQN ALGQMQNIQV
SICMQSAYNE GTLMKFQKIT GDARIPLPLD SFPVPVSTPE GLGTSSNNLG VPATEQRQES
FEGFIARMCS PSPDATSGTG SQRKEEELSR NSRSSSEKKT KTGEYTKKHS DKQHPGKDLH
S*

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

287 / 287

Last intron/exon boundary

2131

Theoretical NMD boundary in CDS

1794

Length of CDS

2166

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

Back to summary table

MutationT@ster 2025

Variant:

9:78266441G>C_4_ENST00000647199

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.50, LOF (oe): 1.16, misssense (oe): 1.12, synonymous (oe): 1.03 ? (gnomAD)

Ensembl transcript ID

ENST00000647199.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1819-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVIWR
HRVGLATKKP VSSGRKHSLG KEYYAPAPLP PGVSGFLPWR TAERAKRHRG FPLIKTRDIC
NQLQQPGFPV TVTVESPSSS EVEEVDDSSE SVHEVPEKTS IEQEALQEKL EECLKQLKEE
RVIRLKVDKR VSELEHENAQ LRNINFSLSE ALHAQSLTNM ILDDEGVLGS IENSFQKFHA
FLDLLKDAGL GQLATMAGID QSDFQLLGHP QMTSTVSNPP KEEKKALEDE KPEPKQNALG
QMQNIQFQKI TGDARIPLPL DSFPVPVSTP EGLGTSSNNL GVPATEQRQE SFEGFIARMC
SPSPDATSGT GSQRKEEELS RNSRSSSEKK TKTESH*

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

272 / 272

Last intron/exon boundary

2351

Theoretical NMD boundary in CDS

2029

Length of CDS

2091

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

Back to summary table

MutationT@ster 2025

Variant:

9:78266441G>C_5_ENST00000643499

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.58, LOF (oe): 1.21, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000643499.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1864-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVIWR
HRGLATKKPV SSGRKHSLGK EYYAPAPLPP GVSGFLPWRT AERAKRHRGF PLIKTRDICN
QLQQPGFPVT VTVESPSSSE VEEVDDSSES VHEVPEKTSI EQEALQEKLE ECLKQLKEER
VIRLKVDKRV SELEHENAQL RNINFSLSEA LHAQSLTNMI LDDEGVLGSI ENSFQKFHAF
LDLLKDAGLG QLATMAGIDQ SDFQLLGHPQ MTSTVSNPPK EEKKALEDEK PEPKQNALGQ
MQNIQVSICM QSAYNEGTLM KFQKITGDAR IPLPLDSFPV PVSTPEGLGT SSNNLGVPAT
EQRQESFEGF IARMCSPSPD ATSGTGSQRK EEELSRNSRS SSEKKTKTGE YTKKHSDKQH
PGKDLHS*

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

244 / 244

Last intron/exon boundary

2106

Theoretical NMD boundary in CDS

1812

Length of CDS

2184

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_6_ENST00000643273

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.53, LOF (oe): 1.19, misssense (oe): 1.12, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000643273.2

Genbank transcript ID

NM_001330691 (exact from MANE), NM_001349839 (by similarity)

UniProt / AlphaMissense peptide

CEP78_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1846-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIGLAT
KKPVSSGRKH SLGKEYYAPA PLPPGVSGFL PWRTAERAKR HRGFPLIKTR DICNQLQQPG
FPVTVTVESP SSSEVEEVDD SSESVHEVPE KTSIEQEALQ EKLEECLKQL KEERVIRLKV
DKRVSELEHE NAQLRNINFS LSEALHAQSL TNMILDDEGV LGSIENSFQK FHAFLDLLKD
AGLGQLATMA GIDQSDFQLL GHPQMTSTVS NPPKEEKKAL EDEKPEPKQN ALGQMQNIQV
SICMQSAYNE GTLMKFQKIT GDARIPLPLD SFPVPVSTPE GLGTSSNNLG VPATEQRQES
FEGFIARMCS PSPDATSGTG SQRKEEELSR NSRSSSEKKT KTESH*

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

277 / 277

Last intron/exon boundary

2383

Theoretical NMD boundary in CDS

2056

Length of CDS

2118

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_7_ENST00000415759

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.51, LOF (oe): 1.14, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000415759.6

Genbank transcript ID

NM_032171 (by similarity)

UniProt / AlphaMissense peptide

CEP78_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1801-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVGLA
TKKPVSSGRK HSLGKEYYAP APLPPGVSGF LPWRTAERAK RHRGFPLIKT RDICNQLQQP
GFPVTVTVES PSSSEVEEVD DSSESVHEVP EKTSIEQEAL QEKLEECLKQ LKEERVIRLK
VDKRVSELEH ENAQLRNINF SLSEALHAQS LTNMILDDEG VLGSIENSFQ KFHAFLDLLK
DAGLGQLATM AGIDQSDFQL LGHPQMTSTV SNPPKEEKKA LEDEKPEPKQ NALGQMQNIQ
FQKITGDARI PLPLDSFPVP VSTPEGLGTS SNNLGVPATE QRQESFEGFI ARMCSPSPDA
TSGTGSQRKE EELSRNSRSS SEKKTKTGEY TKKHSDKQHP GKDLHS*

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

190 / 190

Last intron/exon boundary

1989

Theoretical NMD boundary in CDS

1749

Length of CDS

2121

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_10_ENST00000642669

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.51, LOF (oe): 1.14, misssense (oe): 1.13, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000642669.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CEP78_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1801-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVGLA
TKKPVSSGRK HSLGKEYYAP APLPPGVSGF LPWRTAERAK RHRGFPLIKT RDICNQLQQP
GFPVTVTVES PSSSEVEEVD DSSESVHEVP EKTSIEQEAL QEKLEECLKQ LKEERVIRLK
VDKRVSELEH ENAQLRNINF SLSEALHAQS LTNMILDDEG VLGSIENSFQ KFHAFLDLLK
DAGLGQLATM AGIDQSDFQL LGHPQMTSTV SNPPKEEKKA LEDEKPEPKQ NALGQMQNIQ
FQKITGDARI PLPLDSFPVP VSTPEGLGTS SNNLGVPATE QRQESFEGFI ARMCSPSPDA
TSGTGSQRKE EELSRNSRSS SEKKTKTGEY TKKHSDKQHP GKDLHS*

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

82 / 82

Last intron/exon boundary

1881

Theoretical NMD boundary in CDS

1749

Length of CDS

2121

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

MutationT@ster 2025

Variant:

9:78266441G>C_12_ENST00000643847

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.53, LOF (oe): 1.19, misssense (oe): 1.12, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000643847.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1750-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRD HSMMKAVIKK VLQNGRSAKS EYQWITSPSV KEPSKTAKQK
RRTIILGSGH KGKATIRIVI WRHRGLATKK PVSSGRKHSL GKEYYAPAPL PPGVSGFLPW
RTAERAKRHR GFPLIKTRDI CNQLQQPGFP VTVTVESPSS SEVEEVDDSS ESVHEVPEKT
SIEQEALQEK LEECLKQLKE ERVIRLKVDK RVSELEHENA QLRNINFSLS EALHAQSLTN
MILDDEGVLG SIENSFQKFH AFLDLLKDAG LGQLATMAGI DQSDFQLLGH PQMTSTVSNP
PKEEKKALED EKPEPKQNAL GQMQNIQVSI CMQSAYNEGT LMKFQKITGD ARIPLPLDSF
PVPVSTPEGL GTSSNNLGVP ATEQRQESFE GFIARMCSPS PDATSGTGSQ RKEEELSRNS
RSSSEKKTKT ESH*

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

247 / 247

Last intron/exon boundary

2257

Theoretical NMD boundary in CDS

1960

Length of CDS

2022

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

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MutationT@ster 2025

Variant:

9:78266441G>C_13_ENST00000376598

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Prediction:

DeleteriousPermalink

Summary:

Heterozygous in gnomAD
Splice site lost

Model: without_aae
Tree vote: 185|15 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr9:78266441G>C (GRCh38)

Gene symbol

CEP78

Gene constraints

LOEUF: 1.53, LOF (oe): 1.19, misssense (oe): 1.12, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000376598.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1864-1G>C
g.30380G>C

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	rs146563928
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	12	4877	4889

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.969	0.953
	1.118	0.992
(flanking)	1.665	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor lost	30380	wt: 0.00 / mu: 0.00	-	wt: ttccttctag\|TTTCAGAAAA mu: ttccttctac\|TTTCAGAAAA

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

9

Strand

1

Original gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTAGTTTCAGAAAATTACAGGTGA

Altered gDNA sequence snippet

TTGTTTTGTTTTTCCTTCTACTTTCAGAAAATTACAGGTGA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MIDSVKLRRD SAADFFSHYE YLCALQNSVP LPAVRACLRE GVLDFNADRL RGVDWAPLLS
TLKINKDLPL VSIKSFFQPW LGDTGSDMNK FCRSRVPAIR YKDVTFQLCK ALKGCLSISS
VLKNLELNGL ILRERDLTIL AKGLNKSASL VHLSLANCPI GDGGLEIICQ GIKSSITLKT
VNFTGCNLTW QGADHMAKIL KYQTMRRHEE TWAESLRYRR PDLDCMAGLR RITLNCNTLI
GDLGACAFAD SLSEDLWLRA LDLQQCGLTN EGAKALLEAL ETNTTLVVLD IRKNPLIDHS
MMKAVIKKVL QNGRSAKSEY QWITSPSVKE PSKTAKQKRR TIILGSGHKG KATIRIVIWR
HRGLATKKPV SSGRKHSLGK EYYAPAPLPP GVSGFLPWRT AERAKRHRGF PLIKTRDICN
QLQQPGFPVT VTVESPSSSE VEEVDDSSES VHEVPEKTSI EQEALQEKLE ECLKQLKEER
VIRLKVDKRV SELEHENAQL RNINFSLSEA LHAQSLTNMI LDDEGVLGSI ENSFQKFHAF
LDLLKDAGLG QLATMAGIDQ SDFQLLGHPQ MTSTVSNPPK EEKKALEDEK PEPKQNALGQ
MQNIQVSICM QSAYNEGTLM KFQKITGDAR IPLPLDSFPV PVSTPEGLGT SSNNLGVPAT
EQRQESFEGF IARMCSPSPD ATSGTGSQRK EEELSRNSRS SSEKKTKTES H*

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

1 / 1

Last intron/exon boundary

2125

Theoretical NMD boundary in CDS

2074

Length of CDS

2136

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

30380

Chromosomal position

78266441

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

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