MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 2431610 (pathogenic)
Protein features (might be) affected

Model: complex_aae
Tree vote: 9|1 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.67, LOF (oe): 0.43, misssense (oe): 1.07, synonymous (oe): 1.14 ? (gnomAD)

Ensembl transcript ID

ENST00000314520.6

Genbank transcript ID

NM_005664 (exact from MANE)

UniProt / AlphaMissense peptide

MKRN3_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.476delC
g.585delC

AA changes

P161Rfs*10

Frameshift

Yes

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

Species	Match	AA	Alignment
Human		161	E	P	P	T	Q	E	V	A	E	A	P	P	A	A	S	S	L	S	L	P	V	I	G	S	A	A	E	R	G	F	F	E	A	E	R	D	N	A	D	R	G	A	A	G	G	A	G	V	E	S	W	A	D	A	I	E	F	V	P	G	Q	P	Y	R	G	R	W	V	A	S	A	P	E	A	P	L	Q	S	S	E	T	E	R	K	Q	M	A	V	G	S	G	L	R	F	C	Y	Y	A	S	R	G	V	C	F	R	G	E	S	C	M	Y	L	H	G	D	I	C	D	M	C	G	L	Q	T	L	H	P	M	D	A	A	Q	R	E	E	H	M	R	A	C	I	E	A
mutated	no alignment	n/a
Ptroglodytes	no alignment	n/a
Mmulatta	no alignment	n/a
Fcatus	partly conserved	143	E	T	L	P	Q	E	V	A	K	A	P	S	A	A	P	S	C	S	L	P	V	I	G	L	A	A	E	R	G	F	F	E	A	E	R	D	N	A	G	L	A	A	A	G	G	A	S	V	E	G	W	E	N	A	I	E	F	V	P	G	Q	P	Y	R	G	R	M	V	P	F	V	P	R	A	P	L	Q	S	P	V	T	E	R	E	Q	I	A	V	G	R	G
Mmusculus	partly conserved	158	E	P	P	T	Q	E	V	A	E	A	P	P	A	A	S	S	S	S	L	P	L	I	G	S	A	A	E	R	G	F	T	E	A	E	I	D	N	A	G	I	R	S	A	A	E	R	G	F	S	E	A	E	I	D	N	A	S	L	A	A	G	A	A	A	G	A	G	A	E	G	W	E	G	A	I	E	F	V	P	G	Q	P	Y	R	G	R	M	V	P	P	H
Ggallus	partly conserved	114	K	P	L	M	Q	EEE	L	T	T	V	N	P	A	A	K	T	YPS	D	L	A	L	L	P	E	T	V	E	E	D	I	I	E	I	E	D	E	N	I	D	L	A	A	A	G	-	V	G	A	E	D	W	V	N	A	V	E	F	V	P	G	Q	P	Y	C	G	R	A	A	P	S	C	T	E	V	P	L	E	E	M	V	I	E	E	E	Y	E	K	Q	E	A	D	E
Trubripes	partly conserved	116		P	T	K	S	E	E	V	S	N	P	Q	M	LLL	S	S	T	P	P	P	I	D	P	E	C	S	E	S	G	P	R	L	K	T	Q	D	-	-	-	-	-	-	-	-	-	-	-	-	-	-	W	A	N	A	A	E	F	V	P	G	Q	P	Y	C	G	R	A	E	S	V	D	V	E	I	S	I	P	L	I	E	E	L	N	G	D	A	T	T	D	K	E	E	L	R	K	-	-	-	-	Q	L	C	P	Y	A	A	V	G	E	C	R	Y	G	V	N	C	A	Y	L
Drerio	no homologue
Dmelanogaster	partly conserved	89			Q	Q	R	N	W	A	N	A	P	V	F	V	P	S	Q	K	R	-	-	-	Y	T	A	H	E	Q	S	E	F	E	T	T	V	DP	E	A	V	M	E	A	Q	A	G	A	S	Y	D	T	L	A	P	G	V	S	W	A	E	-	-	-	-	-	-	-	-	V	V	G	G	P	S	S	L	N	K	E	D	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	Y	G	E	E	N	S	S	C	A	W	G	E	F	S	A	Y	P	I	H	M	E	L	C	E	M	C
Celegans	partly conserved	67												T	P	Q	T	S	Q	N	Q	Q	N	L	Q	N	S	G	Q	R	V	R	P	K	Q	L	P	E	-	-	-	-	-	-	-	-	-	-	-	L	K	F	N	A	Q	A	A	E	F	V	PRW	K	M	P	Q	R	GPVT	S	Y	A	G	A	A	A	S	A	D	H	G	E	S	S	S	S	F	Q	S	S	H	E	Q	A	Q	L	M	M	C	P	Y	H	Q	K	S	G	D	C	N	R	Q	D	M	D	C	P	F	A	H	G	N	Y	C	D	M	C	Q	Q	W	S
Xtropicalis	partly conserved	100	K	P	L	K	E	D	L	I	G	N	T	S	T	A	R	S	W	P	S	E	S	P	A	E	P	S	S	N	I	N	S	K	A	A	E	L	A	A	S	E	L	A	A	G	G	P	Q	A	E	D	W	V	N	A	V	E	F	V	P	G	Q	L	Y	S	G	R	-	-	-	-	A	P	D	A	Y	T	Q	G	T	Q	K	E	D	E	C	R	E	Q	P	A	D	P	E	L	K	K	Q	L	C

Protein features

Start (aa)	End (aa)	Feature	Details
1	507	CHAIN		lost
238	265	ZN_FING	C3H1-type	lost
266	293	REGION		lost
311	365	ZN_FING	RING-type	lost
394	423	ZN_FING	C3H1-type	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

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

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP PAASSLSLPV IGSAAERGFF
EAERDNADRG AAGGAGVESW ADAIEFVPGQ PYRGRWVASA PEAPLQSSET ERKQMAVGSG
LRFCYYASRG VCFRGESCMY LHGDICDMCG LQTLHPMDAA QREEHMRACI EAHEKDMELS
FAVQRGMDKV CGICMEVVYE KANPNDRRFG ILSNCNHSFC IRCIRRWRSA RQFENRIVKS
CPQCRVTSEL VIPSEFWVEE EEEKQKLIQQ YKEAMSNKAC RYFAEGRGNC PFGDTCFYKH
EYPEGWGDEP PGPGGGSFSA YWHQLVEPVR MGEGNMLYKS IKKELVVLRL ASLLFKRFLS
LRDELPFSED QWDLLHYELE EYFNLIL*

Mutated AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP RLHPPFPCL*

Position of stopcodon in wt / mu CDS

1524 / 510

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

508 / 170

Position of stopcodon in wt / mu cDNA

1633 / 619

Position of start ATG in wt / mu cDNA

110 / 110

Last intron/exon boundary

0

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

1524

Coding sequence (CDS) position

475 / 477

cDNA position

584 / 586

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

Speed

0.04 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:

15:23566257GC>G_8_ENST00000678440

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 2431610 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.22, LOF (oe): 0.84, misssense (oe): 1.15, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000678440.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.476delC
g.585delC

AA changes

P161Rfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

Species	Match	AA	Alignment
Human		161	E	P	P	T	Q	E	V	A	E	A	P	P	A	A	S	S	L	S	L	P	V	I	G	S
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)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

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

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP PAASSLSLPV IGSAAERGFF
EAERDNADRG AAGGAGVESW ADAIEFVPGQ PYRGRWVASA PEAPLQSSET ERKQMAVGSG
LRFCYYASRG VCFRGESCMY LHGDICDMCG LQTLHPMDAA QREEHMRACI EAHEKDMELS
FAVQRGMDKV YPQVEKCQTV *

Mutated AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP RLHPPFPCL*

Position of stopcodon in wt / mu CDS

963 / 510

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

321 / 170

Position of stopcodon in wt / mu cDNA

963 / 510

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

927

Theoretical NMD boundary in CDS

876

Length of CDS

963

Coding sequence (CDS) position

475 / 477

cDNA position

475 / 477

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

Speed

0.03 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:

15:23566257GC>G_9_ENST00000676568

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Known disease mutation: ClinVar ID 2431610 (pathogenic)
NMD

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

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.26, LOF (oe): 0.85, misssense (oe): 1.15, synonymous (oe): 1.22 ? (gnomAD)

Ensembl transcript ID

ENST00000676568.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.476delC
g.585delC

AA changes

P161Rfs*10

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

Species	Match	AA	Alignment
Human		161	E	P	P	T	Q	E	V	A	E	A	P	P	A	A	S	S	L	S	L	P	V	I	G	S
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)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

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

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered cDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP PAASSLSLPV IGSAAERGFF
EAERDNADRG AAGGAGVESW ADAIEFVPGQ PYRGRWVASA PEAPLQSSET ERKQMAVGSG
LRFCYYASRG VCFRGESCMY LHGDICDMCG LQTLHPMDAA QREEHMRACI EAHEKDMELS
FAVQRGMDKV NGMDSENQEE SQVIKGSVPE *

Mutated AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRYYIHGQCK EGENCRYSHD
LSGRKMATEG GVSPPGASAG GGPSTAAHIE PPTQEVAEAP RLHPPFPCL*

Position of stopcodon in wt / mu CDS

993 / 510

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

331 / 170

Position of stopcodon in wt / mu cDNA

993 / 510

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

927

Theoretical NMD boundary in CDS

876

Length of CDS

993

Coding sequence (CDS) position

475 / 477

cDNA position

475 / 477

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

Speed

0.04 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:

15:23566257GC>G_3_ENST00000564592

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 129|71 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.44, misssense (oe): 1.05, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000564592.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.305+171delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRCIRRWRSA RQFENRIVKS
CPQCRVTSEL VIPSEFWVEE EEEKQKLIQQ YKEAMSNKAC RFTAVKNLPG VSDETLDFGL
LS*

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

109 / 109

Last intron/exon boundary

590

Theoretical NMD boundary in CDS

431

Length of CDS

549

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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

MutationT@ster 2025

Variant:

15:23566257GC>G_7_ENST00000649065

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 129|71 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.82, LOF (oe): 0.44, misssense (oe): 1.05, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000649065.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.305+171delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRCIRRWRSA RQFENRIVKS
CPQCRVTSEL VIPSEFWVEE EEEKQKLIQQ YKEAMSNKAC R*

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

51 / 51

Last intron/exon boundary

532

Theoretical NMD boundary in CDS

431

Length of CDS

486

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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

MutationT@ster 2025

Variant:

15:23566257GC>G_5_ENST00000647595

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 130|70 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.84, LOF (oe): 0.69, misssense (oe): 1.00, synonymous (oe): 0.56 ? (gnomAD)

Ensembl transcript ID

ENST00000647595.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.51+425delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQVNG MDSENQEESQ VIKGSVPE*

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

104 / 104

Last intron/exon boundary

154

Theoretical NMD boundary in CDS

cannot be calculated, distance between start ATG and last intron/exon boundary is too small

Length of CDS

117

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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

MutationT@ster 2025

Variant:

15:23566257GC>G_6_ENST00000568252

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 136|64 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.46, LOF (oe): 0.70, misssense (oe): 1.12, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000568252.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.305+171delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRDIC*

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

67 / 67

Last intron/exon boundary

371

Theoretical NMD boundary in CDS

254

Length of CDS

318

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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

MutationT@ster 2025

Variant:

15:23566257GC>G_2_ENST00000679144

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 151|49 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.30, LOF (oe): 0.57, misssense (oe): 1.13, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000679144.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.305+171delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CR*

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

110 / 110

Last intron/exon boundary

414

Theoretical NMD boundary in CDS

254

Length of CDS

309

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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

MutationT@ster 2025

Variant:

15:23566257GC>G_4_ENST00000677119

Prediction:

DeleteriousPermalink

Summary:

Known disease mutation: ClinVar ID 2431610 (pathogenic)

Model: without_aae
Tree vote: 151|49 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr15:23566258delC (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.30, LOF (oe): 0.57, misssense (oe): 1.13, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000677119.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

intron

DNA changes

c.305+171delC
g.585delC

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Precocious puberty, central, 2

pathogenic

Variant DBs

dbSNP ID	rs763195944
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	0	5	5

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.58	0.01
	0.492	0.003
(flanking)	0.365	0.002

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

15

Strand

1

Original gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCCGGCTGCATCCTCCC

Altered gDNA sequence snippet

GACTCAGGAAGTGGCGGAAGCCCCCCGGCTGCATCCTCCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEEPAAPSEA HEAAGAQAGA EAAREGVSGP DLPVCEPSGE SAAPDSALPH AARGWAPFPV
APVPAHLRRG GLRPAPASGG GAWPSPLPSR SSGIWTKQII CRFTAVKNLP GVSDETLDFG
LLS*

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

109 / 109

Last intron/exon boundary

413

Theoretical NMD boundary in CDS

254

Length of CDS

372

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

584 / 586

Chromosomal position

23566257 / 23566259

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