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
MT speed 0.04 s - this script 2.422241 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
ENST00000392455(MANE Select)	CCDC50	Benign	8\|192	without_aae		Yes				Single base exchange		N/A	Homozygous in gnomAD Splice site changes
ENST00000392456	CCDC50	Benign	9\|191	without_aae		Yes				Single base exchange		N/A	Homozygous in gnomAD Splice site changes

MutationT@ster 2025

Variant:

3:191357084C>G_2_ENST00000392455

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Splice site changes

Model: without_aae
Tree vote: 8|192 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:191357084C>G (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

CCD50_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.50-4C>G
g.28000C>G

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	rs188384
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.493	0
	-0.666	0
(flanking)	4.621	0.995

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	28003	wt: 8.40 / mu: 7.71	-	wt: tctactctag\|TATGCCGAGA mu: tctactgtag\|TATGCCGAGA

Distance from splice site

4

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

CTGTTTTTCCTCCATCTACTCTAGTATGCCGAGATTTTGCT

Altered gDNA sequence snippet

CTGTTTTTCCTCCATCTACTGTAGTATGCCGAGATTTTGCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

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

N/A

gDNA position

28000

Chromosomal position

191357084

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

Back to summary table

MutationT@ster 2025

Variant:

3:191357084C>G_1_ENST00000392456

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD
Splice site changes

Model: without_aae
Tree vote: 9|191 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr3:191357084C>G (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

CCD50_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.50-4C>G
g.28000C>G

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	rs188384
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.493	0
	-0.666	0
(flanking)	4.621	0.995

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	28003	wt: 8.40 / mu: 7.71	-	wt: tctactctag\|TATGCCGAGA mu: tctactgtag\|TATGCCGAGA

Distance from splice site

4

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

3

Strand

1

Original gDNA sequence snippet

CTGTTTTTCCTCCATCTACTCTAGTATGCCGAGATTTTGCT

Altered gDNA sequence snippet

CTGTTTTTCCTCCATCTACTGTAGTATGCCGAGATTTTGCT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

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

N/A

gDNA position

28000

Chromosomal position

191357084

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

Back to summary table