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: ENST00000392456
Querying Taster for transcript #2: ENST00000340524
MT speed 0.03 s - this script 2.373199 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
ENST00000340524(MANE Select)	UTS2B	Benign	1\|199	without_aae		No				Single base exchange		N/A	Heterozygous in gnomAD
ENST00000392456	CCDC50	Benign	2\|97	5utr		No				Single base exchange		N/A	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

3:191329292G>A_2_ENST00000340524

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 1|199 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:191329292G>A (GRCh38)

Gene symbol

UTS2B

Gene constraints

LOEUF: 1.59, LOF (oe): 0.65, misssense (oe): 1.13, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000340524.10

Genbank transcript ID

NM_198152 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-664-583C>T
g.1235C>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	rs186382346
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	2	750	752

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.144	0.026
	1.62	0.059
(flanking)	0.984	0.051

?

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

3

Strand

-1

Original gDNA sequence snippet

GTAACCGCAATTGCGAGTGGCTGGCGAGCGAAGATCAGCGC

Altered gDNA sequence snippet

GTAACCGCAATTGCGAGTGGTTGGCGAGCGAAGATCAGCGC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNKILSSTVC FGLLTLLSVL SFLQSVHGRP YLTQGNEIFP DKKYTNREEL LLALLNKNFD
FQRPFNTDLA LPNKLEELNQ LEKLKEQLVE EKDSETSYAV DGLFSSHPSK RACFWKYCV*

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

778 / 778

Last intron/exon boundary

1111

Theoretical NMD boundary in CDS

283

Length of CDS

360

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

1235

Chromosomal position

191329292

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:

3:191329292G>A_1_ENST00000392456

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 5utr
Tree vote: 2|97 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:191329292G>A (GRCh38)

Gene symbol

CCDC50

Gene constraints

LOEUF: 0.89, LOF (oe): 0.64, misssense (oe): 0.91, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000392456.4

Genbank transcript ID

NM_174908 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.208G>A
g.208G>A

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	rs186382346
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	2	750	752

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.144	0.026
	1.62	0.059
(flanking)	0.984	0.051

?

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

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

GCGCTGATCTTCGCTCGCCAGCCACTCGCAATTGCGGTTAC

Altered gDNA sequence snippet

GCGCTGATCTTCGCTCGCCAACCACTCGCAATTGCGGTTAC

Original cDNA sequence snippet

GCGCTGATCTTCGCTCGCCAGCCACTCGCAATTGCGGTTAC

Altered cDNA sequence snippet

GCGCTGATCTTCGCTCGCCAACCACTCGCAATTGCGGTTAC

Wildtype AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGG MKPRVMKEAV STPSRMAHRD QEWYDAEIAR
KLQEEELLAT QVDMRAAQVA QDEEIARLLM AEEKKAYKKA KEREKSSLDK RKQDPEWKPK
TAKAANSKSK ESDEPHHSKN ERPARPPPPI MTDGEDADYT HFTNQQSSTR HFSKSESSHK
GFHYKH*

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

591 / 591

Last intron/exon boundary

1491

Theoretical NMD boundary in CDS

850

Length of CDS

921

Coding sequence (CDS) position

N/A

cDNA position

208

gDNA position

208

Chromosomal position

191329292

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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