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: ENST00000397054
Querying Taster for transcript #2: ENST00000296388
Querying Taster for transcript #3: ENST00000236040
MT speed 0.17 s - this script 2.57378 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000397054	P3H1	Deleterious	61\|39	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000236040	P3H1	Deleterious	63\|37	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000296388(MANE Select)	P3H1	Benign	43\|57	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

1:42750266C>A_1_ENST00000397054

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 61|39 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:42750266C>A (GRCh38)

Gene symbol

P3H1

Gene constraints

LOEUF: 1.03, LOF (oe): 0.85, misssense (oe): 0.92, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000397054.7

Genbank transcript ID

NM_001146289 (by similarity)

UniProt / AlphaMissense peptide

P3H1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1640G>T
g.16819G>T

AA changes

AAE:	R547L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs750685729
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		547	H	L	Y	Y	N	V	T	E	K	V	R	R	I	M	E	S	Y	F	R	L	D	T	P	L
mutated	not conserved	547						V	T	E	K	V	R	L	I	M	E	S	Y	F	R	L	D	T	P
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
23	736	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.482	0
	0.589	0.041
(flanking)	3.377	0.385

?

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

1

Strand

-1

Original gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Original cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Wildtype AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRRIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERVRAAR AGQGAGR*

Mutated AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRLIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERVRAAR AGQGAGR*

Position of stopcodon in wt / mu CDS

2094 / 2094

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

698 / 698

Position of stopcodon in wt / mu cDNA

2207 / 2207

Position of start ATG in wt / mu cDNA

114 / 114

Last intron/exon boundary

2187

Theoretical NMD boundary in CDS

2023

Length of CDS

2094

Coding sequence (CDS) position

1640

cDNA position

1753

gDNA position

16819

Chromosomal position

42750266

Speed

0.05 s

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

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MutationT@ster 2025

Variant:

1:42750266C>A_3_ENST00000236040

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 63|37 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:42750266C>A (GRCh38)

Gene symbol

P3H1

Gene constraints

LOEUF: 1.05, LOF (oe): 0.85, misssense (oe): 0.90, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000236040.8

Genbank transcript ID

NM_001243246 (by similarity)

UniProt / AlphaMissense peptide

P3H1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1640G>T
g.16819G>T

AA changes

AAE:	R547L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs750685729
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		547	H	L	Y	Y	N	V	T	E	K	V	R	R	I	M	E	S	Y	F	R	L	D	T	P	L
mutated	not conserved	547						V	T	E	K	V	R	L	I	M	E	S	Y	F	R	L	D	T	P
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
23	736	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.482	0
	0.589	0.041
(flanking)	3.377	0.385

?

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

1

Strand

-1

Original gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Original cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Wildtype AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRRIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERVRAAR AGESSWCCGD PFPERPWFAF LFPKSHCQWL
RHERSTWDTS SNALSLWSHC LVLPGPAVNG IQVGKEVKTG SDAEFLVPSL GPTSAVLFQR
VGPAGKEMSL GPLRNLPCPL GSSS*

Mutated AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRLIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERVRAAR AGESSWCCGD PFPERPWFAF LFPKSHCQWL
RHERSTWDTS SNALSLWSHC LVLPGPAVNG IQVGKEVKTG SDAEFLVPSL GPTSAVLFQR
VGPAGKEMSL GPLRNLPCPL GSSS*

Position of stopcodon in wt / mu CDS

2415 / 2415

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

805 / 805

Position of stopcodon in wt / mu cDNA

2456 / 2456

Position of start ATG in wt / mu cDNA

42 / 42

Last intron/exon boundary

1955

Theoretical NMD boundary in CDS

1863

Length of CDS

2415

Coding sequence (CDS) position

1640

cDNA position

1681

gDNA position

16819

Chromosomal position

42750266

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

Back to summary table

MutationT@ster 2025

Variant:

1:42750266C>A_2_ENST00000296388

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 43|57 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:42750266C>A (GRCh38)

Gene symbol

P3H1

Gene constraints

LOEUF: 1.05, LOF (oe): 0.86, misssense (oe): 0.91, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000296388.10

Genbank transcript ID

NM_022356 (exact from MANE)

UniProt / AlphaMissense peptide

P3H1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1640G>T
g.16819G>T

AA changes

AAE:	R547L	?
Score:	102

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs750685729
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		547	H	L	Y	Y	N	V	T	E	K	V	R	R	I	M	E	S	Y	F	R	L	D	T	P	L
mutated	not conserved	547						V	T	E	K	V	R	L	I	M	E	S	Y	F	R	L	D	T	P
Ptroglodytes	all identical	547						V	T	E	K	V	R	R	I	M	E	S	Y	F	R	L	D	T	P
Mmulatta	all identical	547						V	T	E	K	V	R	R	I	M	E	S	Y	F	R	L	D	T	P
Fcatus	all identical	594						V	T	E	K	V	R	R	V	M	E	S	Y	F	R	L	D	T	P
Mmusculus	all identical	550			Y	Y	N	V	T	E	K	V	R	R	V	M	E	S	Y	F	R	L	D	T	P
Ggallus	not conserved	540	H	L	Y	Y	N	V	T	E	K	V	R	H	M	M	E	S	Y	F	R	L	E	V	P
Trubripes	all identical	533	R	A	F	F	D	V	S	E	K	A	R	R	I	L	E	L	Y	F	Q	L	K	T	P
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	536	L	L	Y	Y	N	V	T	D	K	V	R	R	V	V	E	S	Y	F	R	L	D	S	P

Protein features

Start (aa)	End (aa)	Feature	Details
23	736	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.482	0
	0.589	0.041
(flanking)	3.377	0.385

?

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

1

Strand

-1

Original gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered gDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Original cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCGCATCATGGAGTCCTACTTCC

Altered cDNA sequence snippet

CGTGACGGAGAAGGTGCGGCTCATCATGGAGTCCTACTTCC

Wildtype AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRRIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERDRVQA DDLVKMLFSP EEMDLSQEQP LDAQQGPPEP
AQESLSGSES KPKDEL*

Mutated AA sequence

MAVRALKLLT TLLAVVAAAS QAEVESEAGW GMVTPDLLFA EGTAAYARGD WPGVVLSMER
ALRSRAALRA LRLRCRTQCA ADFPWELDPD WSPSPAQASG AAALRDLSFF GGLLRRAACL
RRCLGPPAAH SLSEEMELEF RKRSPYNYLQ VAYFKINKLE KAVAAAHTFF VGNPEHMEMQ
QNLDYYQTMS GVKEADFKDL ETQPHMQEFR LGVRLYSEEQ PQEAVPHLEA ALQEYFVAYE
ECRALCEGPY DYDGYNYLEY NADLFQAITD HYIQVLNCKQ NCVTELASHP SREKPFEDFL
PSHYNYLQFA YYNIGNYTQA VECAKTYLLF FPNDEVMNQN LAYYAAMLGE EHTRSIGPRE
SAKEYRQRSL LEKELLFFAY DVFGIPFVDP DSWTPEEVIP KRLQEKQKSE RETAVRISQE
IGNLMKEIET LVEEKTKESL DVSRLTREGG PLLYEGISLT MNSKLLNGSQ RVVMDGVISD
HECQELQRLT NVAATSGDGY RGQTSPHTPN EKFYGVTVFK ALKLGQEGKV PLQSAHLYYN
VTEKVRLIME SYFRLDTPLY FSYSHLVCRT AIEEVQAERK DDSHPVHVDN CILNAETLVC
VKEPPAYTFR DYSAILYLNG DFDGGNFYFT ELDAKTVTAE VQPQCGRAVG FSSGTENPHG
VKAVTRGQRC AIALWFTLDP RHSERDRVQA DDLVKMLFSP EEMDLSQEQP LDAQQGPPEP
AQESLSGSES KPKDEL*

Position of stopcodon in wt / mu CDS

2211 / 2211

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

737 / 737

Position of stopcodon in wt / mu cDNA

2268 / 2268

Position of start ATG in wt / mu cDNA

58 / 58

Last intron/exon boundary

2112

Theoretical NMD boundary in CDS

2004

Length of CDS

2211

Coding sequence (CDS) position

1640

cDNA position

1697

gDNA position

16819

Chromosomal position

42750266

Speed

0.05 s

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

Back to summary table