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: ENST00000314397
Querying Taster for transcript #2: ENST00000274606
MT speed 0.03 s - this script 2.371581 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
ENST00000314397	NHP2	Benign	0\|200	without_aae		No				Single base exchange		N/A	Heterozygous in gnomAD
ENST00000274606(MANE Select)	NHP2	Benign	0\|200	without_aae		No				Single base exchange		N/A	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

5:178153647G>A_1_ENST00000314397

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:178153647G>A (GRCh38)

Gene symbol

NHP2

Gene constraints

LOEUF: 1.07, LOF (oe): 0.57, misssense (oe): 0.86, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000314397.9

Genbank transcript ID

NM_001034833 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.160+11C>T
g.248C>T

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	rs201274409
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	4	3074	3078

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.588	0
	-1.909	0.001
(flanking)	-0.071	0.008

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

ATCAAGAAAGGTGAGGCGGACGGCGGCGTGGCCGGGATGGG

Altered gDNA sequence snippet

ATCAAGAAAGGTGAGGCGGATGGCGGCGTGGCCGGGATGGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTKIKADPDG PEAQAEACSG ERTYQELLVN QNPIAQPLAS RRLTRKLYKC IKKAVKQKQI
RRGVKEVQKF VNKGEKGTWV QPQAPSAPPV *

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

32 / 32

Last intron/exon boundary

261

Theoretical NMD boundary in CDS

179

Length of CDS

273

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

248

Chromosomal position

178153647

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:

5:178153647G>A_2_ENST00000274606

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:178153647G>A (GRCh38)

Gene symbol

NHP2

Gene constraints

LOEUF: 1.12, LOF (oe): 0.68, misssense (oe): 0.88, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000274606.8

Genbank transcript ID

NM_017838 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.160+11C>T
g.248C>T

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	rs201274409
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	4	3074	3078

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.588	0
	-1.909	0.001
(flanking)	-0.071	0.008

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

11

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

-1

Original gDNA sequence snippet

ATCAAGAAAGGTGAGGCGGACGGCGGCGTGGCCGGGATGGG

Altered gDNA sequence snippet

ATCAAGAAAGGTGAGGCGGATGGCGGCGTGGCCGGGATGGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MTKIKADPDG PEAQAEACSG ERTYQELLVN QNPIAQPLAS RRLTRKLYKC IKKAVKQKQI
RRGVKEVQKF VNKGEKGIMV LAGDTLPIEV YCHLPVMCED RNLPYVYIPS KTDLGAAAGS
KRPTCVIMVK PHEEYQEAYD ECLEEVQSLP LPL*

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

69 / 69

Last intron/exon boundary

404

Theoretical NMD boundary in CDS

285

Length of CDS

462

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

248

Chromosomal position

178153647

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

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