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: ENST00000392455
Querying Taster for transcript #3: ENST00000340524
MT speed 0.06 s - this script 2.427727 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
ENST00000340524(MANE Select)	UTS2B	Benign	3\|197	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000392456	CCDC50	Benign	23\|75	5utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000392455(MANE Select)	CCDC50	Benign	24\|75	5utr	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

3:191329453C>T_3_ENST00000340524

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 3|197 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:191329453C>T (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.-664-744G>A
g.1074G>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	rs56141214
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	49	4738	4787

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.298	1
	0.089	0.996
(flanking)	0.545	0.998

?

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

GGCGGCCCAGCTGCCCCGCCGCGGCCACCTGCTCCGCGTCC

Altered gDNA sequence snippet

GGCGGCCCAGCTGCCCCGCCACGGCCACCTGCTCCGCGTCC

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

1074

Chromosomal position

191329453

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:

3:191329453C>T_1_ENST00000392456

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 23|75 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:191329453C>T (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.369C>T
g.369C>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	rs56141214
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	49	4738	4787

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.298	1
	0.089	0.996
(flanking)	0.545	0.998

?

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

GGACGCGGAGCAGGTGGCCGCGGCGGGGCAGCTGGGCCGCC

Altered gDNA sequence snippet

GGACGCGGAGCAGGTGGCCGTGGCGGGGCAGCTGGGCCGCC

Original cDNA sequence snippet

GGACGCGGAGCAGGTGGCCGCGGCGGGGCAGCTGGGCCGCC

Altered cDNA sequence snippet

GGACGCGGAGCAGGTGGCCGTGGCGGGGCAGCTGGGCCGCC

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

369

gDNA position

369

Chromosomal position

191329453

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

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MutationT@ster 2025

Variant:

3:191329453C>T_2_ENST00000392455

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 24|75 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:191329453C>T (GRCh38)

Gene symbol

CCDC50

Gene constraints

LOEUF: 0.93, LOF (oe): 0.72, misssense (oe): 0.94, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000392455.9

Genbank transcript ID

NM_178335 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.60C>T
g.369C>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	rs56141214
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	49	4738	4787

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.298	1
	0.089	0.996
(flanking)	0.545	0.998

?

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

GGACGCGGAGCAGGTGGCCGCGGCGGGGCAGCTGGGCCGCC

Altered gDNA sequence snippet

GGACGCGGAGCAGGTGGCCGTGGCGGGGCAGCTGGGCCGCC

Original cDNA sequence snippet

GGACGCGGAGCAGGTGGCCGCGGCGGGGCAGCTGGGCCGCC

Altered cDNA sequence snippet

GGACGCGGAGCAGGTGGCCGTGGCGGGGCAGCTGGGCCGCC

Wildtype AA sequence

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGD QPGSRRAREL GSGFSRPCRL QRDGKTVKHK
KEKPEHPLEN LEEPEQHCSS KRSLSSSSSG KGRDNPHINN EQHERKRSTQ ERPRRPLLPT
ISGEVFLSTE CDDWETKINH QTRNWEKQSR HQDRLSPKSS QKAGLHCKEV VYGRDHGQGE
HRKRRHRPRT PPFSESEEQL HLHDAGMKPR VMKEAVSTPS RMAHRDQEWY DAEIARKLQE
EELLATQVDM RAAQVAQDEE IARLLMAEEK KAYKKAKERE KSSLDKRKQD PEWKPKTAKA
ANSKSKESDE PHHSKNERPA RPPPPIMTDG EDADYTHFTN QQSSTRHFSK SESSHKGFHY
KH*

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

282 / 282

Last intron/exon boundary

1710

Theoretical NMD boundary in CDS

1378

Length of CDS

1449

Coding sequence (CDS) position

N/A

cDNA position

60

gDNA position

369

Chromosomal position

191329453

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

Back to summary table