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: ENST00000513335
Querying Taster for transcript #2: ENST00000325106
Querying Taster for transcript #3: ENST00000504425
MT speed 1.08 s - this script 3.499636 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Amino acid changes	Variant type	Protein length	Features at a glance
ENST00000513335	TTC29	Deleterious	10\|0	complex_aae	No	Y276*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000504425	TTC29	Deleterious	10\|0	complex_aae	No	Y250*	Single base exchange	NMD	Amino acid sequence changed NMD
ENST00000325106(MANE Select)	TTC29	Deleterious	10\|0	complex_aae	No	Y250*	Single base exchange	NMD	Amino acid sequence changed NMD Protein features (might be) affected

MutationT@ster 2025

Variant:

4:146874765G>C_1_ENST00000513335

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr4:146874765G>C (GRCh38)

Gene symbol

TTC29

Gene constraints

LOEUF: 0.88, LOF (oe): 0.63, misssense (oe): 1.01, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000513335.5

Genbank transcript ID

NM_001300761 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.828C>G
g.71118C>G

AA changes

Y276* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		276	L	L	S	D	K	M	L	E	N	K	E	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	A	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	D	T	Y	C	K	I	S	T	D	L	D	D	D
mutated	partly conserved	194	N	S	E	D	K	W	V	R	N	H	F	Y	E	R	C	F	K	I	-	-	-	-	A	Q	L	I	K	I	D	C	G	K	K	-	E	A	E	A	H	M	H	M	G	L	L	Y	E	E	D	G	Q	L	L	E	A	A	E	H	Y	E
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.425	1
	4.37	1
(flanking)	3.237	1

?

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

4

Strand

-1

Original gDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered gDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Original cDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered cDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Wildtype AA sequence

MIPMFTVTLE DSGTLWKSLH SSSESEMTTL PPLPMTRPKL TALARQKLPC SSRKIPRSQL
IKEKDDIDHY LEVNFKGLSK EEVAAYRNSY KKNICVDMLR DGYHKSFTEL FALMERWDAL
REAARVRSLF WLQKPLEEQP DKLDYLYHYL TRAEDAERKE SFEDVHNNLY ALACYFNNSE
DKWVRNHFYE RCFKIAQLIK IDCGKKEAEA HMHMGLLYEE DGQLLEAAEH YEAFHQLTQG
RIWKDETGRS LNLLACESLL RTYRLLSDKM LENKEYKQAI KILIKASEIA KEGSDKKMEA
EASYYLGLAH LAAEEYETAL TVLDTYCKIS TDLDDDLSLG RGYEAIAKVL QSQGEMTEAI
KYLKKFVKIA RNNFQSLDLV RASTMLGDIY NEKGYYNKAS ECFQQAFDTT VELMSMPLMD
ETKVHYGIAK AHQMMLTVNN YIESADLTSL NYLLSWKESR GNIEPDPVTE EFRGSTVEAV
SQNSERLEEL SRFPGDQKNE T*

Mutated AA sequence

MIPMFTVTLE DSGTLWKSLH SSSESEMTTL PPLPMTRPKL TALARQKLPC SSRKIPRSQL
IKEKDDIDHY LEVNFKGLSK EEVAAYRNSY KKNICVDMLR DGYHKSFTEL FALMERWDAL
REAARVRSLF WLQKPLEEQP DKLDYLYHYL TRAEDAERKE SFEDVHNNLY ALACYFNNSE
DKWVRNHFYE RCFKIAQLIK IDCGKKEAEA HMHMGLLYEE DGQLLEAAEH YEAFHQLTQG
RIWKDETGRS LNLLACESLL RTYRLLSDKM LENKE*

Position of stopcodon in wt / mu CDS

1506 / 828

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

502 / 276

Position of stopcodon in wt / mu cDNA

1706 / 1028

Position of start ATG in wt / mu cDNA

201 / 201

Last intron/exon boundary

1675

Theoretical NMD boundary in CDS

1424

Length of CDS

1506

Coding sequence (CDS) position

828

cDNA position

1028

gDNA position

71118

Chromosomal position

146874765

Speed

0.43 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:

4:146874765G>C_3_ENST00000504425

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr4:146874765G>C (GRCh38)

Gene symbol

TTC29

Gene constraints

LOEUF: 0.89, LOF (oe): 0.62, misssense (oe): 1.02, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000504425.5

Genbank transcript ID

NM_001317806 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.750C>G
g.71118C>G

AA changes

Y250* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		250	L	L	S	D	K	M	L	E	N	K	E	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	A	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	D	T	Y	C	K	I	S	T	D	L	D	D	D
mutated	partly conserved	168	N	S	E	D	K	W	V	R	N	H	F	Y	E	R	C	F	K	I	-	-	-	-	A	Q	L	I	K	I	D	C	G	K	K	-	E	A	E	A	H	M	H	M	G	L	L	Y	E	E	D	G	Q	L	L	E	A	A	E	H	Y	E
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.425	1
	4.37	1
(flanking)	3.237	1

?

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

4

Strand

-1

Original gDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered gDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Original cDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered cDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Wildtype AA sequence

MTTLPPLPMT RPKLTALARQ KLPCSSRKIP RSQLIKEKDD IDHYLEVNFK GLSKEEVAAY
RNSYKKNICV DMLRDGYHKS FTELFALMER WDALREAARV RSLFWLQKPL EEQPDKLDYL
YHYLTRAEDA ERKESFEDVH NNLYALACYF NNSEDKWVRN HFYERCFKIA QLIKIDCGKK
EAEAHMHMGL LYEEDGQLLE AAEHYEAFHQ LTQGRIWKDE TGRSLNLLAC ESLLRTYRLL
SDKMLENKEY KQAIKILIKA SEIAKEGSDK KMEAEASYYL GLAHLAAEEY ETALTVLDTY
CKISTDLDDD LSLGRGYEAI AKVLQSQGEM TEAIKYLKKF VKIARNNFQS LDLVRASTML
GDIYNEKGYY NKASECFQQA FDTTVELMSM PLMDETKVHY GIAKAHQMML TVNNYIESAD
LTSLNYLLSW KESRGNIEPD PVTEFRGSTV EAVSQNSERL EELSRFPGDQ KNET*

Mutated AA sequence

MTTLPPLPMT RPKLTALARQ KLPCSSRKIP RSQLIKEKDD IDHYLEVNFK GLSKEEVAAY
RNSYKKNICV DMLRDGYHKS FTELFALMER WDALREAARV RSLFWLQKPL EEQPDKLDYL
YHYLTRAEDA ERKESFEDVH NNLYALACYF NNSEDKWVRN HFYERCFKIA QLIKIDCGKK
EAEAHMHMGL LYEEDGQLLE AAEHYEAFHQ LTQGRIWKDE TGRSLNLLAC ESLLRTYRLL
SDKMLENKE*

Position of stopcodon in wt / mu CDS

1425 / 750

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

475 / 250

Position of stopcodon in wt / mu cDNA

1652 / 977

Position of start ATG in wt / mu cDNA

228 / 228

Last intron/exon boundary

1621

Theoretical NMD boundary in CDS

1343

Length of CDS

1425

Coding sequence (CDS) position

750

cDNA position

977

gDNA position

71118

Chromosomal position

146874765

Speed

0.25 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:

4:146874765G>C_2_ENST00000325106

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to NMD

Analysed issue

Analysis result

Variant

Chr4:146874765G>C (GRCh38)

Gene symbol

TTC29

Gene constraints

LOEUF: 0.89, LOF (oe): 0.62, misssense (oe): 1.02, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000325106.9

Genbank transcript ID

NM_031956 (exact from MANE)

UniProt / AlphaMissense peptide

TTC29_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.750C>G
g.71118C>G

AA changes

Y250* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		250	L	L	S	D	K	M	L	E	N	K	E	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	A	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	D	T	Y	C	K	I	S	T	D	L	D	D	D	L	S	L	G	R	G	Y	E	A	I	A	K	V	L	Q	S	Q	G	E	M	T	E	A	I	K	Y	L	K	K	F	V	K	I	A	R	N	N	F	Q	S	L	D	L	V	R	A	S	T	M	L	G	D	I	Y	N	E	K	G	Y	Y	N	K
mutated	partly conserved	168	N	S	E	D	K	W	V	R	N	H	F	Y	E	R	C	F	K	I	-	-	-	-	A	Q	L	I	K	I	D	C	G	K	K	-	E	A	E	A	H	M	H	M	G	L	L	Y	E	E	D	G	Q	L	L	E	A	A	E	H	Y	E
Ptroglodytes	partly conserved	250			S	D	K	M	L	E	N	K	E	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	A	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	D	T	Y	C	K	I	S	T	D	L	D	D	D	L	S	L	G	R	G	Y	E	A	I	A	K	V	L	Q	S	Q	G	E	M	T	E	A	I	K	Y	L	K	K	F	V	K	I	A	R	K	N	F	Q	S	L	D	L	V	R	A	S	T	M	L
Mmulatta	partly conserved	250			S	D	K	M	L	Q	N	K	E	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	G	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	D	T	Y	C	K	I	S	T	E	L	D	D	D	L	S	L	G	R	A	Y	E	A	I	A	K	V	L	Q	S	Q	G	N	T	T	E	A	I	K	Y	L	K	K	F	V	K	I	A	R	N	N	F	Q	S	L	D	F	V	R	A	S	T	M	L
Fcatus	partly conserved	250			S	D	K	M	L	E	N	K	E	Y	K	Q	A	I	R	I	L	I	K	A	S	E	I	A	K	E	G	S	D	K	K	M	E	G	E	A	S	Y	Y	L	G	L	A	H	L	A	A	E	E	Y	E	T	A	L	T	V	L	N	T	Y	S	K	I	S	I	D	L	E	D	D	L	S	L	G	R	A	Y	E	A	I	A	K	V	L	Q	S	Q	G	N	M	P	E	A	I	K	Y	L	K	K	V	V	E	I	A	R	N	N	F	Q	S	L	D	V	M	R	A	S	T	M	L
Mmusculus	partly conserved	250			S	D	R	M	L	E	N	K	D	Y	K	Q	A	I	K	I	L	I	K	A	S	E	I	A	R	E	G	N	D	R	S	M	E	G	E	A	S	Y	Y	L	G	L	A	H	L	A	S	G	E	Y	E	T	A	L	T	V	L	N	R	Y	S	E	I	S	T	S	L	D	D	D	H	G	L	G	R	A	Y	E	A	I	A	K	A	L	Q	S	Q	G	E	T	T	E	A	I	N	Y	L	E	K	F	V	T	I	A	R	N	N	L	Q	S	L	D	M	I	R	A	C	T	M	L
Ggallus	partly conserved	250			A	D	K	M	L	E	N	K	E	Q	Q	Q	A	I	K	T	L	I	K	A	I	R	M	A	K	T	G	G	D	K	K	M	E	G	E	A	A	Y	C	L	S	L	V	Y	H	F	A	G	E	E	K	T	A	L	S	I	L	N	T	S	I	K	I	F	T	A	L	H	D	S	A	G	L	K	R	A	Y	E	A	T	D	K	I	L	V	S	Q	G	K	V	A	E	S	L	T	Y	L	E	E	F	K	K	V	A	E	N	A	N	L	S	Q	S	V	V	D	A	C	V	L	I
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	partly conserved	257	L	Q	S	D	K	M	L	A	N	K	E	C	Q	Q	A	I	K	T	L	I	K	A	F	D	M	A	R	E	G	G	N	K	K	L	E	G	E	A	A	Y	R	L	G	L	A	H	I	S	S	G	N	P	Q	T	A	I	T	Y	L	N	T	Y	M	E	I	S	K	M	L	E	D	N	V	S	L	G	K	A	Y	K	A	M	A	K	A	L	E	S	Q	G	K	I	L	E	S	V	E	Y	L	E	N	F	I	K	I	A	K	L	N	N	L	N	Q	S	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	475	CHAIN		lost
234	267	REPEAT	TPR	lost
274	307	REPEAT	TPR	lost
314	347	REPEAT	TPR	lost
354	387	REPEAT	TPR	lost
437	475	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.425	1
	4.37	1
(flanking)	3.237	1

?

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

4

Strand

-1

Original gDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered gDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Original cDNA sequence snippet

ATGCTAGAAAATAAAGAATACAAACAGGCCATCAAAATTCT

Altered cDNA sequence snippet

ATGCTAGAAAATAAAGAATAGAAACAGGCCATCAAAATTCT

Wildtype AA sequence

MTTLPPLPMT RPKLTALARQ KLPCSSRKIP RSQLIKEKDD IDHYLEVNFK GLSKEEVAAY
RNSYKKNICV DMLRDGYHKS FTELFALMER WDALREAARV RSLFWLQKPL EEQPDKLDYL
YHYLTRAEDA ERKESFEDVH NNLYALACYF NNSEDKWVRN HFYERCFKIA QLIKIDCGKK
EAEAHMHMGL LYEEDGQLLE AAEHYEAFHQ LTQGRIWKDE TGRSLNLLAC ESLLRTYRLL
SDKMLENKEY KQAIKILIKA SEIAKEGSDK KMEAEASYYL GLAHLAAEEY ETALTVLDTY
CKISTDLDDD LSLGRGYEAI AKVLQSQGEM TEAIKYLKKF VKIARNNFQS LDLVRASTML
GDIYNEKGYY NKASECFQQA FDTTVELMSM PLMDETKVHY GIAKAHQMML TVNNYIESAD
LTSLNYLLSW KESRGNIEPD PVTEEFRGST VEAVSQNSER LEELSRFPGD QKNET*

Mutated AA sequence

MTTLPPLPMT RPKLTALARQ KLPCSSRKIP RSQLIKEKDD IDHYLEVNFK GLSKEEVAAY
RNSYKKNICV DMLRDGYHKS FTELFALMER WDALREAARV RSLFWLQKPL EEQPDKLDYL
YHYLTRAEDA ERKESFEDVH NNLYALACYF NNSEDKWVRN HFYERCFKIA QLIKIDCGKK
EAEAHMHMGL LYEEDGQLLE AAEHYEAFHQ LTQGRIWKDE TGRSLNLLAC ESLLRTYRLL
SDKMLENKE*

Position of stopcodon in wt / mu CDS

1428 / 750

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

476 / 250

Position of stopcodon in wt / mu cDNA

1637 / 959

Position of start ATG in wt / mu cDNA

210 / 210

Last intron/exon boundary

1606

Theoretical NMD boundary in CDS

1346

Length of CDS

1428

Coding sequence (CDS) position

750

cDNA position

959

gDNA position

71118

Chromosomal position

146874765

Speed

0.40 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