MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000315266
Querying Taster for transcript #2: ENST00000478722
Querying Taster for transcript #3: ENST00000459628
Querying Taster for transcript #4: ENST00000543237
MT speed 0.08 s - this script 2.408258 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length
ENST00000315266	GPHN	Benign	20\|180	without_aae	No	Single base exchange	N/A
ENST00000478722(MANE Select)	GPHN	Benign	20\|180	without_aae	No	Single base exchange	N/A
ENST00000543237	GPHN	Benign	20\|180	without_aae	No	Single base exchange	N/A
ENST00000459628	GPHN	Benign	24\|176	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

14:66508599G>C_1_ENST00000315266

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 20|180 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:66508599G>C (GRCh38)

Gene symbol

GPHN

Gene constraints

LOEUF: 0.24, LOF (oe): 0.09, misssense (oe): 0.64, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000315266.9

Genbank transcript ID

NM_001377519 (by similarity), NM_001377515 (by similarity), NM_001377516 (by similarity), NM_001377518 (by similarity), NM_001377517 (by similarity), NM_001024218 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.64+8G>C
g.1193G>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	rs201245603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	122	123

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.192	0.159
	2.647	0.317
(flanking)	0.639	0.138

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

8

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

14

Strand

1

Original gDNA sequence snippet

GGAGTCCTTACAGGTAACCGGGGGAGGAGGTCTGGGACCTA

Altered gDNA sequence snippet

GGAGTCCTTACAGGTAACCGCGGGAGGAGGTCTGGGACCTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEGMILTN HDHQIRVGVL TVSDSCFRNL AEDRSGINLK DLVQDPSLLG GTISAYKIVP
DEIEEIKETL IDWCDEKELN LILTTGGTGF APRDVTPEAT KEVIEREAPG MALAMLMGSL
NVTPLGMLSR PVCGIRGKTL IINLPGSKKG SQECFQFILP ALPHAIDLLR DAIVKVKEVH
DELEDLPSPP PPLSPPPTTS PHKQTEDKGV QCEEEEEEKK DSGVASTEDS SSSHITAAAI
AAKIPDSIIS RGVQVLPRDT ASLSTTPSES PRAQATSRLS TASCPTPKVQ SRCSSKENIL
RASHSAVDIT KVARRHRMSP FPLTSMDKAF ITVLEMTPVL GTEIINYRDG MGRVLAQDVY
AKDNLPPFPA SVKDGYAVRA ADGPGDRFII GESQAGEQPT QTVMPGQVMR VTTGAPIPCG
ADAVVQVEDT ELIRESDDGT EELEVRILVQ ARPGQDIRPI GHDIKRGECV LAKGTHMGPS
EIGLLATVGV TEVEVNKFPV VAVMSTGNEL LNPEDDLLPG KIRDSNRSTL LATIQEHGYP
TINLGIVGDN PDDLLNALNE GISRADVIIT SGGVSMGEKD YLKQVLDIDL HAQIHFGRVF
MKPGLPTTFA TLDIDGVRKI IFALPGNPVS AVVTCNLFVV PALRKMQGIL DPRPTIIKAR
LSCDVKLDPR PEYHRCILTW HHQEPLPWAQ STGNQMSSRL MSMRSANGLL MLPPKTEQYV
ELHKGEVVDV MVIGRL*

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

1122 / 1122

Last intron/exon boundary

3198

Theoretical NMD boundary in CDS

2026

Length of CDS

2211

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1193

Chromosomal position

66508599

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

14:66508599G>C_2_ENST00000478722

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 20|180 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:66508599G>C (GRCh38)

Gene symbol

GPHN

Gene constraints

LOEUF: 0.24, LOF (oe): 0.09, misssense (oe): 0.64, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000478722.6

Genbank transcript ID

NM_020806 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.64+8G>C
g.1193G>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	rs201245603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	122	123

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.192	0.159
	2.647	0.317
(flanking)	0.639	0.138

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

8

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

14

Strand

1

Original gDNA sequence snippet

GGAGTCCTTACAGGTAACCGGGGGAGGAGGTCTGGGACCTA

Altered gDNA sequence snippet

GGAGTCCTTACAGGTAACCGCGGGAGGAGGTCTGGGACCTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEGMILTN HDHQIRVGVL TVSDSCFRNL AEDRSGINLK DLVQDPSLLG GTISAYKIVP
DEIEEIKETL IDWCDEKELN LILTTGGTGF APRDVTPEAT KEVIEREAPG MALAMLMGSL
NVTPLGMLSR PVCGIRGKTL IINLPGSKKG SQECFQFILP ALPHAIDLLR DAIVKVKEVH
DELEDLPSPP PPLSPPPTTS PHKQTEDKGV QCEEEEEEKK DSGVASTEDS SSSHITAAAI
AAKKHPFYTS PAVVMAHGEQ PIPGLINYSH HSTDERIPDS IISRGVQVLP RDTASLSTTP
SESPRAQATS RLSTASCPTP KVQSRCSSKE NILRASHSAV DITKVARRHR MSPFPLTSMD
KAFITVLEMT PVLGTEIINY RDGMGRVLAQ DVYAKDNLPP FPASVKDGYA VRAADGPGDR
FIIGESQAGE QPTQTVMPGQ VMRVTTGAPI PCGADAVVQV EDTELIRESD DGTEELEVRI
LVQARPGQDI RPIGHDIKRG ECVLAKGTHM GPSEIGLLAT VGVTEVEVNK FPVVAVMSTG
NELLNPEDDL LPGKIRDSNR STLLATIQEH GYPTINLGIV GDNPDDLLNA LNEGISRADV
IITSGGVSMG EKDYLKQVLD IDLHAQIHFG RVFMKPGLPT TFATLDIDGV RKIIFALPGN
PVSAVVTCNL FVVPALRKMQ GILDPRPTII KARLSCDVKL DPRPEYHRCI LTWHHQEPLP
WAQSTGNQMS SRLMSMRSAN GLLMLPPKTE QYVELHKGEV VDVMVIGRL*

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

382 / 382

Last intron/exon boundary

2557

Theoretical NMD boundary in CDS

2125

Length of CDS

2310

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1193

Chromosomal position

66508599

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:

14:66508599G>C_4_ENST00000543237

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 20|180 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:66508599G>C (GRCh38)

Gene symbol

GPHN

Gene constraints

LOEUF: 0.24, LOF (oe): 0.09, misssense (oe): 0.64, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000543237.5

Genbank transcript ID

NM_001377514 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.64+8G>C
g.1193G>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	rs201245603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	122	123

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.192	0.159
	2.647	0.317
(flanking)	0.639	0.138

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

8

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

14

Strand

1

Original gDNA sequence snippet

GGAGTCCTTACAGGTAACCGGGGGAGGAGGTCTGGGACCTA

Altered gDNA sequence snippet

GGAGTCCTTACAGGTAACCGCGGGAGGAGGTCTGGGACCTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEGMILTN HDHQIRVGVL TVSDSCFRNL AEDRSGINLK DLVQDPSLLG GTISAYKIVP
DEIEEIKETL IDWCDEKELN LILTTGGTGF APRDVTPEKF PTFPFCGLQK GATKEVIERE
APGMALAMLM GSLNVTPLGM LSRPVCGIRG KTLIINLPGS KKGSQECFQF ILPALPHAID
LLRDAIVKVK EVHDELEDLP SPPPPLSPPP TTSPHKQTED KGVQCEEEEE EKKDSGVAST
EDSSSSHITA AAIAAKIPDS IISRGVQVLP RDTASLSTTP SESPRAQATS RLSTASCPTP
KQIRRPDESK GVASRVGSLK ARLPSCSSTY SVSEVQSRCS SKENILRASH SAVDITKVAR
RHRMSPFPLT SMDKAFITVL EMTPVLGTEI INYRDGMGRV LAQDVYAKDN LPPFPASVKD
GYAVRAADGP GDRFIIGESQ AGEQPTQTVM PGQVMRVTTG APIPCGADAV VQVEDTELIR
ESDDGTEELE VRILVQARPG QDIRPIGHDI KRGECVLAKG THMGPSEIGL LATVGVTEVE
VNKFPVVAVM STGNELLNPE DDLLPGKIRD SNRSTLLATI QEHGYPTINL GIVGDNPDDL
LNALNEGISR ADVIITSGGV SMGEKDYLKQ VLDIDLHAQI HFGRVFMKPG LPTTFATLDI
DGVRKIIFAL PGNPVSAVVT CNLFVVPALR KMQGILDPRP TIIKARLSCD VKLDPRPEYH
RCILTWHHQE PLPWAQSTGN QMSSRLMSMR SANGLLMLPP KTEQYVELHK GEVVDVMVIG
RL*

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

25 / 25

Last intron/exon boundary

2239

Theoretical NMD boundary in CDS

2164

Length of CDS

2349

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1193

Chromosomal position

66508599

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:

14:66508599G>C_3_ENST00000459628

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 24|176 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:66508599G>C (GRCh38)

Gene symbol

GPHN

Gene constraints

LOEUF: 0.30, LOF (oe): 0.06, misssense (oe): 0.74, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000459628.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.64+8G>C
g.1193G>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	rs201245603
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	1	122	123

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.192	0.159
	2.647	0.317
(flanking)	0.639	0.138

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

8

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

14

Strand

1

Original gDNA sequence snippet

GGAGTCCTTACAGGTAACCGGGGGAGGAGGTCTGGGACCTA

Altered gDNA sequence snippet

GGAGTCCTTACAGGTAACCGCGGGAGGAGGTCTGGGACCTA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MATEGMILTN HDHQIRVGVL TVSDSCFRNL AEDRSGINLK DLVQDPSLLG GTISAYKIVP
DEIEEIKKFP TFPFCGLQKG ATKEVIEREA PGMALAMLMG SLNVTPLGML SRPVCGIRGK
TLIINLPGSK KGSQECFQFI LPALPHAIDL LRDAIVKVKE VHDELEDLPS PPPPLSPPPT
TSPHKQTEDK GVQCEEEEEE KKDSGVASTE DSSSSHITAA AIAAKKHPFY TSPAVVMAHG
EQPIPGLINY SHHSTDERIP DSIISRGVQV LPRDTASLST TPSESPRAQA TSRLSTASCP
TPKVQSRCSS KENILRASHS AVDITKVARR HRMSPFPLTS MDKAFITVLE MTPVLGTEII
NYRGTIIFDH CPFFSSFFSK *

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

391 / 391

Last intron/exon boundary

1342

Theoretical NMD boundary in CDS

901

Length of CDS

1143

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1193

Chromosomal position

66508599

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