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: ENST00000642620
Querying Taster for transcript #2: ENST00000647044
MT speed 0.08 s - this script 2.567162 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000642620(MANE Select)	NDP	Deleterious	10\|0	complex_aae		No	Yes		C96*	Single base exchange		Strongly truncated protein, might cause NMD (-38 AA / more than 10% missing)	Amino acid sequence changed Known disease mutation: ClinVar ID 1459580 (pathogenic) Protein features (might be) affected Truncated protein (might cause NMD)
ENST00000647044	NDP	Deleterious	10\|0	complex_aae		No	Yes		C96*	Single base exchange		Strongly truncated protein, might cause NMD (-38 AA / more than 10% missing)	Amino acid sequence changed Known disease mutation: ClinVar ID 1459580 (pathogenic) Protein features (might be) affected Truncated protein (might cause NMD)

MutationT@ster 2025

Variant:

23:43949913G>T_1_ENST00000642620

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 1459580 (pathogenic)
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:43949913G>T (GRCh38)

Gene symbol

NDP

Gene constraints

no data

Ensembl transcript ID

ENST00000642620.1

Genbank transcript ID

NM_000266 (exact from MANE)

UniProt / AlphaMissense peptide

NDP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.288C>A
g.23483C>A

AA changes

AAE:

C96*

R97-

P98-

Q99-

T100-

S101-

K102-

L103-

K104-

A105-

L106-

R107-

L108-

R109-

C110-

S111-

G112-

G113-

M114-

R115-

L116-

T117-

A118-

T119-

Y120-

R121-

Y122-

I123-

L124-

S125-

C126-

H127-

C128-

E129-

E130-

C131-

N132-

S133-

*134-

?

Score:

-

Frameshift

No

Length of protein

Strongly truncated protein, might cause NMD (-38 AA / more than 10% missing)

Pathogenic variant (ClinVar)

not provided

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		96	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L	R	C	S	G	G	M	R	L	T	A	T	Y	R	Y	I	L	S	C	H	C	E	E	C	N	S	*
mutated	no alignment	n/a
Ptroglodytes	all conserved	96	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L	R	C	S	G	G	M	R	L	T	A	T	Y	R	Y	I	L	S	C	H	C	E	E	C	N	S
Mmulatta	all conserved	96	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L	R	C	S	G	G	M	R	L	T	A	T	Y	R	Y	I	L	S	C	H	C	E	E	C	N	S
Fcatus	partly conserved	96	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L	R	C	S	G	G	M	R	L	T	A	T	Y	R	Y	I	L	S	C	H	C	E	E	C	G	S
Mmusculus	all conserved	94	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L	R	C	S	G	G	M	R	L	T	A	T	Y	R	Y	I	L	S	C	H	C	E	E	C	S	S
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
25	133	CHAIN		lost
39	132	DOMAIN	CTCK	lost
94	110	STRAND		lost
111	113	TURN		lost
115	133	STRAND		lost
131	131	DISULFID		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

-1

Original gDNA sequence snippet

CGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCT

Altered gDNA sequence snippet

CGTTCCTCCTGTCACTGCTGACGGCCCCAGACTTCCAAGCT

Original cDNA sequence snippet

CGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCT

Altered cDNA sequence snippet

CGTTCCTCCTGTCACTGCTGACGGCCCCAGACTTCCAAGCT

Wildtype AA sequence

MRKHVLAASF SMLSLLVIMG DTDSKTDSSF IMDSDPRRCM RHHYVDSISH PLYKCSSKMV
LLARCEGHCS QASRSEPLVS FSTVLKQPFR SSCHCCRPQT SKLKALRLRC SGGMRLTATY
RYILSCHCEE CNS*

Mutated AA sequence

MRKHVLAASF SMLSLLVIMG DTDSKTDSSF IMDSDPRRCM RHHYVDSISH PLYKCSSKMV
LLARCEGHCS QASRSEPLVS FSTVLKQPFR SSCHC*

Position of stopcodon in wt / mu CDS

402 / 288

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

134 / 96

Position of stopcodon in wt / mu cDNA

696 / 582

Position of start ATG in wt / mu cDNA

295 / 295

Last intron/exon boundary

468

Theoretical NMD boundary in CDS

123

Length of CDS

402

Coding sequence (CDS) position

288

cDNA position

582

gDNA position

23483

Chromosomal position

43949913

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

Back to summary table

MutationT@ster 2025

Variant:

23:43949913G>T_2_ENST00000647044

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 1459580 (pathogenic)
Protein features (might be) affected
Truncated protein (might cause NMD)

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:43949913G>T (GRCh38)

Gene symbol

NDP

Gene constraints

no data

Ensembl transcript ID

ENST00000647044.1

Genbank transcript ID

UniProt / AlphaMissense peptide

NDP_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.288C>A
g.23483C>A

AA changes

AAE:

C96*

R97-

P98-

Q99-

T100-

S101-

K102-

L103-

K104-

A105-

L106-

R107-

L108-

R109-

C110-

S111-

G112-

G113-

M114-

R115-

L116-

T117-

A118-

T119-

Y120-

R121-

Y122-

I123-

L124-

S125-

C126-

H127-

C128-

E129-

E130-

C131-

N132-

S133-

*134-

?

Score:

-

Frameshift

No

Length of protein

Strongly truncated protein, might cause NMD (-38 AA / more than 10% missing)

Pathogenic variant (ClinVar)

not provided

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'T' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		96	L	K	Q	P	F	R	S	S	C	H	C	C	R	P	Q	T	S	K	L	K	A	L	R	L
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
25	133	CHAIN		lost
39	132	DOMAIN	CTCK	lost
94	110	STRAND		lost
111	113	TURN		lost
115	133	STRAND		lost
131	131	DISULFID		lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

-1

Original gDNA sequence snippet

CGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCT

Altered gDNA sequence snippet

CGTTCCTCCTGTCACTGCTGACGGCCCCAGACTTCCAAGCT

Original cDNA sequence snippet

CGTTCCTCCTGTCACTGCTGCCGGCCCCAGACTTCCAAGCT

Altered cDNA sequence snippet

CGTTCCTCCTGTCACTGCTGACGGCCCCAGACTTCCAAGCT

Wildtype AA sequence

MRKHVLAASF SMLSLLVIMG DTDSKTDSSF IMDSDPRRCM RHHYVDSISH PLYKCSSKMV
LLARCEGHCS QASRSEPLVS FSTVLKQPFR SSCHCCRPQT SKLKALRLRC SGGMRLTATY
RYILSCHCEE CNS*

Mutated AA sequence

MRKHVLAASF SMLSLLVIMG DTDSKTDSSF IMDSDPRRCM RHHYVDSISH PLYKCSSKMV
LLARCEGHCS QASRSEPLVS FSTVLKQPFR SSCHC*

Position of stopcodon in wt / mu CDS

402 / 288

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

134 / 96

Position of stopcodon in wt / mu cDNA

796 / 682

Position of start ATG in wt / mu cDNA

395 / 395

Last intron/exon boundary

568

Theoretical NMD boundary in CDS

123

Length of CDS

402

Coding sequence (CDS) position

288

cDNA position

682

gDNA position

23483

Chromosomal position

43949913

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

Back to summary table