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: ENST00000599111
Querying Taster for transcript #2: ENST00000354276
Querying Taster for transcript #3: ENST00000599921
MT speed 0.27 s - this script 2.730652 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
ENST00000599111	PLA2G4C	Deleterious	74\|26	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000599921(MANE Select)	PLA2G4C	Deleterious	74\|26	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000354276	PLA2G4C	Benign	29\|71	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

19:48052998C>T_1_ENST00000599111

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 74|26 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:48052998C>T (GRCh38)

Gene symbol

PLA2G4C

Gene constraints

LOEUF: 1.15, LOF (oe): 0.89, misssense (oe): 0.92, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000599111.5

Genbank transcript ID

NM_001159322 (by similarity)

UniProt / AlphaMissense peptide

PA24C_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1609G>A
g.57820G>A

AA changes

AAE:	G537R	?
Score:	125

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs371948216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	156	156

Protein conservation

Species	Match	AA	Alignment
Human		537	K	K	I	L	R	E	L	M	N	V	A	G	L	Y	Y	P	K	D	S	A	R	S	C	C
mutated	not conserved	537	K	K	I	L	R	E	L	M	N	V	A	R	L	Y	Y
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	538	CHAIN		lost
1	541	DOMAIN	PLA2c	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.234	0.031
	-0.022	0.025
(flanking)	0.122	0.026

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	57821	wt: 8.53 / mu: 10.28	-	wt: ACGTGGCCGG\|gtaggtggga mu: ACGTGGCCAG\|gtaggtggga

Distance from splice site

2

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

-1

Original gDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGTAGGTGGGAGACCATAGT

Altered gDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGTAGGTGGGAGACCATAGT

Original cDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGCTCTACTACCCGAAGGAT

Altered cDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGCTCTACTACCCGAAGGAT

Wildtype AA sequence

MRTRPRPRLR RTENFLTAVH HGKKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG
GGLRAHIACL GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT
RQEWDLAKSL QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP
IFAAIDNDLQ PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER
DLTFLRGLWG SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES
SQGEHPPPED EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI
CASKWEWGTT HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF
DFSAGDPFET IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF
NIDACGGDIE AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVAGLYY
PKDSARSCCL A*

Mutated AA sequence

MRTRPRPRLR RTENFLTAVH HGKKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG
GGLRAHIACL GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT
RQEWDLAKSL QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP
IFAAIDNDLQ PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER
DLTFLRGLWG SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES
SQGEHPPPED EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI
CASKWEWGTT HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF
DFSAGDPFET IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF
NIDACGGDIE AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVARLYY
PKDSARSCCL A*

Position of stopcodon in wt / mu CDS

1656 / 1656

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

552 / 552

Position of stopcodon in wt / mu cDNA

1958 / 1958

Position of start ATG in wt / mu cDNA

303 / 303

Last intron/exon boundary

1912

Theoretical NMD boundary in CDS

1559

Length of CDS

1656

Coding sequence (CDS) position

1609

cDNA position

1911

gDNA position

57820

Chromosomal position

48052998

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

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MutationT@ster 2025

Variant:

19:48052998C>T_3_ENST00000599921

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 74|26 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:48052998C>T (GRCh38)

Gene symbol

PLA2G4C

Gene constraints

LOEUF: 1.13, LOF (oe): 0.86, misssense (oe): 0.89, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000599921.6

Genbank transcript ID

NM_003706 (exact from MANE)

UniProt / AlphaMissense peptide

PA24C_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1579G>A
g.57820G>A

AA changes

AAE:	G527R	?
Score:	125

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs371948216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	156	156

Protein conservation

Species	Match	AA	Alignment
Human		527	K	K	I	L	R	E	L	M	N	V	A	G	L	Y	Y	P	K	D	S	A	R	S	C	C
mutated	not conserved	527	K	K	I	L	R	E	L	M	N	V	A	R	L	Y	Y	P	K	D	S	A	R	S	C
Ptroglodytes	all identical	527	K	K	I	L	R	E	L	M	N	V	A	G	L	Y	Y	P	K	D	S	A	R	S	C
Mmulatta	not conserved	529	K	K	I	L	R	E	M	R	N	A	A	M	KD	H	W	D	K	M	R	L	K	S
Fcatus	no homologue
Mmusculus	all identical	569	I	N	I	L	S	E	M	R	K	V	A	G
Ggallus	no homologue
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	538	CHAIN		lost
1	541	DOMAIN	PLA2c	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.234	0.031
	-0.022	0.025
(flanking)	0.122	0.026

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor weakened	57821	wt: 8.53 / mu: 10.28	-	wt: ACGTGGCCGG\|gtaggtggga mu: ACGTGGCCAG\|gtaggtggga

Distance from splice site

2

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

-1

Original gDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGTAGGTGGGAGACCATAGT

Altered gDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGTAGGTGGGAGACCATAGT

Original cDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGCTCTACTACCCGAAGGAT

Altered cDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGCTCTACTACCCGAAGGAT

Wildtype AA sequence

MGSSEVSIIP GLQKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG GGLRAHIACL
GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT RQEWDLAKSL
QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP IFAAIDNDLQ
PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER DLTFLRGLWG
SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES SQGEHPPPED
EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI CASKWEWGTT
HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF DFSAGDPFET
IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF NIDACGGDIE
AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVAGLYY PKDSARSCCL
A*

Mutated AA sequence

MGSSEVSIIP GLQKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG GGLRAHIACL
GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT RQEWDLAKSL
QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP IFAAIDNDLQ
PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER DLTFLRGLWG
SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES SQGEHPPPED
EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI CASKWEWGTT
HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF DFSAGDPFET
IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF NIDACGGDIE
AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVARLYY PKDSARSCCL
A*

Position of stopcodon in wt / mu CDS

1626 / 1626

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

542 / 542

Position of stopcodon in wt / mu cDNA

1989 / 1989

Position of start ATG in wt / mu cDNA

364 / 364

Last intron/exon boundary

1943

Theoretical NMD boundary in CDS

1529

Length of CDS

1626

Coding sequence (CDS) position

1579

cDNA position

1942

gDNA position

57820

Chromosomal position

48052998

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

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MutationT@ster 2025

Variant:

19:48052998C>T_2_ENST00000354276

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 29|71 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:48052998C>T (GRCh38)

Gene symbol

PLA2G4C

Gene constraints

LOEUF: 1.13, LOF (oe): 0.86, misssense (oe): 0.88, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000354276.7

Genbank transcript ID

NM_001159323 (by similarity)

UniProt / AlphaMissense peptide

PA24C_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1579G>A
g.57820G>A

AA changes

AAE:	G527R	?
Score:	125

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs371948216
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	156	156

Protein conservation

Species	Match	AA	Alignment
Human		527	K	K	I	L	R	E	L	M	N	V	A	G	*
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	538	CHAIN		lost
1	541	DOMAIN	PLA2c	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.234	0.031
	-0.022	0.025
(flanking)	0.122	0.026

?

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

19

Strand

-1

Original gDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGTAGGTGGGAGACCATAGT

Altered gDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGTAGGTGGGAGACCATAGT

Original cDNA sequence snippet

GAGAGTTGATGAACGTGGCCGGGTAGGTGGGAGACCATAGT

Altered cDNA sequence snippet

GAGAGTTGATGAACGTGGCCAGGTAGGTGGGAGACCATAGT

Wildtype AA sequence

MGSSEVSIIP GLQKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG GGLRAHIACL
GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT RQEWDLAKSL
QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP IFAAIDNDLQ
PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER DLTFLRGLWG
SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES SQGEHPPPED
EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI CASKWEWGTT
HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF DFSAGDPFET
IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF NIDACGGDIE
AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVAG*

Mutated AA sequence

MGSSEVSIIP GLQKEEKAAV ERRRLHVLKA LKKLRIEADE APVVAVLGSG GGLRAHIACL
GVLSEMKEQG LLDAVTYLAG VSGSTWAISS LYTNDGDMEA LEADLKHRFT RQEWDLAKSL
QKTIQAARSE NYSLTDFWAY MVISKQTREL PESHLSNMKK PVEEGTLPYP IFAAIDNDLQ
PSWQEARAPE TWFEFTPHHA GFSALGAFVS ITHFGSKFKK GRLVRTHPER DLTFLRGLWG
SALGNTEVIR EYIFDQLRNL TLKGLWRRAV ANAKSIGHLI FARLLRLQES SQGEHPPPED
EGGEPEHTWL TEMLENWTRT SLEKQEQPHE DPERKGSLSN LMDFVKKTGI CASKWEWGTT
HNFLYKHGGI RDKIMSSRKH LHLVDAGLAI NTPFPLVLPP TREVHLILSF DFSAGDPFET
IRATTDYCRR HKIPFPQVEE AELDLWSKAP ASCYILKGET GPVVMHFPLF NIDACGGDIE
AWSDTYDTFK LADTYTLDVV VLLLALAKKN VRENKKKILR ELMNVAR*

Position of stopcodon in wt / mu CDS

1584 / 1584

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

528 / 528

Position of stopcodon in wt / mu cDNA

1912 / 1912

Position of start ATG in wt / mu cDNA

329 / 329

Last intron/exon boundary

1951

Theoretical NMD boundary in CDS

1572

Length of CDS

1584

Coding sequence (CDS) position

1579

cDNA position

1907

gDNA position

57820

Chromosomal position

48052998

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

Back to summary table