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 0.05 s - this script 2.483189 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	Deleterious	54\|46	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000392456	CCDC50	Benign	4\|196	without_aae		No				Single base exchange		N/A	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

3:191375230C>T_2_ENST00000392455

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:191375230C>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

CCD50_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.617C>T
g.46146C>T

AA changes

AAE:	S206F	?
Score:	155

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs138153104
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	3	1952	1955

Protein conservation

Species	Match	AA	Alignment
Human		206	E	Q	H	C	S	S	K	R	S	L	S	S	S	S	S	G	K	G	R	D	N	P	H	I
mutated	not conserved	206	E	Q	H	C	S	S	K	R	S	L	S	F	S	S	S	G	K	G	R	D	N	P	H
Ptroglodytes	all identical	206	E	Q	H	C	S	S	K	R	S	L	S	S	S	S	S	G	K	G	R	D	N	P	H
Mmulatta	all identical	215			H	R	S	S	E	R	S	L	S	S	S	S	S	G	K	E	R	D	K	P	Q
Fcatus	all identical	206	E	D	Y	C	S	S	G	K	L	L	S	S	C	S	S	S	K	V	R	G	S	P	Q
Mmusculus	all identical	205	E	E	H	H	P	S	E	R	S	L	P	S	A	S	W	G	R	G	R	D	G	A	Q
Ggallus	not conserved	239	S	E	A	T	N	S	H	R	Q	E	C	K	S	A	S	Q	G	G	S	G	R	PTSLVLEREADRGAGE	H
Trubripes	not conserved	220	E	H	H	L	L	D	E	G	G	W	S	SHGDPYSEQLL	T	S	R	G	KRGDRY
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	all identical	196	K	F	V	R	Q	R	G	R	S	V	E	S	R	S	S	N	K	E	E	DSY	N	V	H

Protein features

Start (aa)	End (aa)	Feature	Details
2	306	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.301	0.011
	3.807	0.035
(flanking)	-0.351	0

?

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

3

Strand

1

Original gDNA sequence snippet

ATCGAAGAGATCCCTGTCATCCTCTAGCTCGGGCAAAGGGA

Altered gDNA sequence snippet

ATCGAAGAGATCCCTGTCATTCTCTAGCTCGGGCAAAGGGA

Original cDNA sequence snippet

ATCGAAGAGATCCCTGTCATCCTCTAGCTCGGGCAAAGGGA

Altered cDNA sequence snippet

ATCGAAGAGATCCCTGTCATTCTCTAGCTCGGGCAAAGGGA

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

MAEVSIDQSK LPGVKEVCRD FAVLEDHTLA HSLQEQEIEH HLASNVQRNR LVQHDLQVAK
QLQEEDLKAQ AQLQKRYKDL EQQDCEIAQE IQEKLAIEAE RRRIQEKKDE DIARLLQEKE
LQEEKKRKKH FPEFPATRAY ADSYYYEDGD QPGSRRAREL GSGFSRPCRL QRDGKTVKHK
KEKPEHPLEN LEEPEQHCSS KRSLSFSSSG 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*

Position of stopcodon in wt / mu CDS

1449 / 1449

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

483 / 483

Position of stopcodon in wt / mu cDNA

1730 / 1730

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

617

cDNA position

898

gDNA position

46146

Chromosomal position

191375230

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:

3:191375230C>T_1_ENST00000392456

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Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: without_aae
Tree vote: 4|196 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:191375230C>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

intron

DNA changes

c.449-4929C>T
g.46146C>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	rs138153104
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	3	1952	1955

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.301	0.011
	3.807	0.035
(flanking)	-0.351	0

?

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

ATCGAAGAGATCCCTGTCATCCTCTAGCTCGGGCAAAGGGA

Altered gDNA sequence snippet

ATCGAAGAGATCCCTGTCATTCTCTAGCTCGGGCAAAGGGA

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

46146

Chromosomal position

191375230

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