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: ENST00000673965
Querying Taster for transcript #2: ENST00000381870
Querying Taster for transcript #3: ENST00000673669
Querying Taster for transcript #4: ENST00000574776
Querying Taster for transcript #5: ENST00000488623
Querying Taster for transcript #6: ENST00000046640
Querying Taster for transcript #7: ENST00000399306
MT speed 0.38 s - this script 2.846365 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000574776	CTNS	Benign	7\|193	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000673669	CTNS	Benign	8\|92	5utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000488623	CTNS	Benign	10\|88	5utr	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000381870	CTNS	Benign	49\|51	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000673965	CTNS	Benign	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000046640(MANE Select)	CTNS	Benign	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000399306	CTNS	Benign	64\|36	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD

MutationT@ster 2025

Variant:

17:3647506G>A_4_ENST00000574776

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 7|193 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.82, LOF (oe): 0.54, misssense (oe): 0.90, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000574776.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-113+7239G>A
g.11048G>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	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

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

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MNWRRKSVIG LSFDFVALNL TGFVAYSVFN IGLLWVPYIK EQFLLKYPNG VNPVNSNDVF
FSLHAVVLTL IIIVQCCLYE RGGQRVSWPA IGFLVLAWLF AFVTMIVAAV GVTTWLQFLF
CFSYIKLAVT LVKYFPQAYM NFYYKSTEGW SIGNVLLDFT GGSFSLLQMF LQSYNNDQWT
LIFGDPTKFG LGVFSIVFDV VFFIQHFCLY RKRPGLQAAR TGSGSRLRQD WAPSLQPKAL
PQTTSVSASS LKG*

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

506 / 506

Last intron/exon boundary

1149

Theoretical NMD boundary in CDS

593

Length of CDS

762

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

11048

Chromosomal position

3647506

Speed

0.04 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:

17:3647506G>A_3_ENST00000673669

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 8|92 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.72, LOF (oe): 0.43, misssense (oe): 0.92, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000673669.1

Genbank transcript ID

NM_001374493 (by similarity), NM_001374495 (by similarity), NM_001374494 (by similarity), NM_001374496 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.379G>A
g.11048G>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	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTTG

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTTG

Wildtype AA sequence

MNWRRKSVIG LSFDFVALNL TGFVAYSVFN IGLLWVPYIK EQFLLKYPNG VNPVNSNDVF
FSLHAVVLTL IIIVQCCLYE RGGQRVSWPA IGFLVLAWLF AFVTMIVAAV GVTTWLQFLF
CFSYIKLAVT LVKYFPQAYM NFYYKSTEGW SIGNVLLDFT GGSFSLLQMF LQSYNNDQWT
LIFGDPTKFG LGVFSIVFDV VFFIQHFCLY RKRPGYDQLN *

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

612 / 612

Last intron/exon boundary

1140

Theoretical NMD boundary in CDS

478

Length of CDS

663

Coding sequence (CDS) position

N/A

cDNA position

379

gDNA position

11048

Chromosomal position

3647506

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

MutationT@ster 2025

Variant:

17:3647506G>A_5_ENST00000488623

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 10|88 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.76, LOF (oe): 0.36, misssense (oe): 0.96, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000488623.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.366G>A
g.11048G>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	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCA

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGCCA

Wildtype AA sequence

MIVAAVGVTT WLQFLFCFSY IKLAVTLVKY FPQAYMNFYY KSTEGWSIGN VLLDFTGGSF
SLLQMFLQSY NNDQWTLIFG DPTKFGLGVF SIVFDVVFFI QHFCLYRKRP GYDQLN*

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

970 / 970

Last intron/exon boundary

1186

Theoretical NMD boundary in CDS

166

Length of CDS

351

Coding sequence (CDS) position

N/A

cDNA position

366

gDNA position

11048

Chromosomal position

3647506

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

MutationT@ster 2025

Variant:

17:3647506G>A_2_ENST00000381870

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 49|51 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.81, LOF (oe): 0.58, misssense (oe): 0.91, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000381870.8

Genbank transcript ID

NM_001031681 (by similarity), NM_001374492 (by similarity)

UniProt / AlphaMissense peptide

CTNS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124G>A
g.11048G>A

AA changes

AAE:	V42I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

Species	Match	AA	Alignment
Human		42	V	V	K	L	E	N	G	S	S	T	N	V	S	L	T	L	R	P	P	L	N	A	T	L
mutated	all conserved	42	V	V	K	L	E	N	G	S	S	T	N	I	S	L	T	L	R	P	P	L	N	A	T
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

Start (aa)	End (aa)	Feature	Details
23	125	TOPO_DOM	Lumenal	lost
23	367	CHAIN		lost
39	43	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCA

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGCCA

Wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGLQAARTGS GSRLRQDWAP SLQPKALPQT TSVSASSLKG *

Mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NISLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGLQAARTGS GSRLRQDWAP SLQPKALPQT TSVSASSLKG *

Position of stopcodon in wt / mu CDS

1203 / 1203

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

401 / 401

Position of stopcodon in wt / mu cDNA

1682 / 1682

Position of start ATG in wt / mu cDNA

480 / 480

Last intron/exon boundary

1564

Theoretical NMD boundary in CDS

1034

Length of CDS

1203

Coding sequence (CDS) position

124

cDNA position

603

gDNA position

11048

Chromosomal position

3647506

Speed

0.14 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:

17:3647506G>A_1_ENST00000673965

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 51|49 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.75, LOF (oe): 0.53, misssense (oe): 0.92, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000673965.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CTNS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124G>A
g.11048G>A

AA changes

AAE:	V42I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

Species	Match	AA	Alignment
Human		42	V	V	K	L	E	N	G	S	S	T	N	V	S	L	T	L	R	P	P	L	N	A	T	L
mutated	all conserved	42	V	V	K	L	E	N	G	S	S	T	N	I	S	L	T	L	R	P	P	L	N	A	T
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

Start (aa)	End (aa)	Feature	Details
23	125	TOPO_DOM	Lumenal	lost
23	367	CHAIN		lost
39	43	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCA

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGCCA

Wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

Mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NISLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

Position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

Position of stopcodon in wt / mu cDNA

1578 / 1578

Position of start ATG in wt / mu cDNA

475 / 475

Last intron/exon boundary

1444

Theoretical NMD boundary in CDS

919

Length of CDS

1104

Coding sequence (CDS) position

124

cDNA position

598

gDNA position

11048

Chromosomal position

3647506

Speed

0.04 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:

17:3647506G>A_6_ENST00000046640

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 51|49 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 0.75, LOF (oe): 0.53, misssense (oe): 0.92, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000046640.9

Genbank transcript ID

NM_004937 (exact from MANE)

UniProt / AlphaMissense peptide

CTNS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124G>A
g.11048G>A

AA changes

AAE:	V42I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

Species	Match	AA	Alignment
Human		42	V	V	K	L	E	N	G	S	S	T	N	V	S	L	T	L	R	P	P	L	N	A	T	L
mutated	all conserved	42	V	V	K	L	E	N	G	S	S	T	N	I	S	L	T	L	R	P	P	L	N	A	T
Ptroglodytes	all identical	42	V	V	K	L	E	N	G	S	S	T	S	V	S	V	T	L	R	P	P	L	N	A	T
Mmulatta	all identical	42	V	V	K	L	E	N	G	S	S	T	N	V	S	I	A	L	R	P	P	L	N	A	T
Fcatus	all conserved	42	T	V	K	L	E	N	G	S	S	A	N	I	S	I	T	L	Q	R	P	L	N	A	T
Mmusculus	all identical	42	T	V	K	L	E	N	G	S	S	T	N	V	D	I	T	L	G	H	P	L	N	S	T
Ggallus	all identical	53	V	V	L	L	E	N	G	S	S	T	N	V	T	I	S	L	R	A	P	L	N	D	T
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	all conserved	255	V	V	T	I	E	N	G	R	S	E	N	I	S	I	T	V	N	C	P	L	N	E	S

Protein features

Start (aa)	End (aa)	Feature	Details
23	125	TOPO_DOM	Lumenal	lost
23	367	CHAIN		lost
39	43	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCA

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGCCA

Wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

Mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NISLTLRPPL NATLVITFEI
TFRSKNITIL ELPDEVVVPP GVTNSSFQVT SQNVGQLTVY LHGNHSNQTG PRIRFLVIRS
SAISIINQVI GWIYFVAWSI SFYPQVIMNW RRKSVIGLSF DFVALNLTGF VAYSVFNIGL
LWVPYIKEQF LLKYPNGVNP VNSNDVFFSL HAVVLTLIII VQCCLYERGG QRVSWPAIGF
LVLAWLFAFV TMIVAAVGVT TWLQFLFCFS YIKLAVTLVK YFPQAYMNFY YKSTEGWSIG
NVLLDFTGGS FSLLQMFLQS YNNDQWTLIF GDPTKFGLGV FSIVFDVVFF IQHFCLYRKR
PGYDQLN*

Position of stopcodon in wt / mu CDS

1104 / 1104

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

368 / 368

Position of stopcodon in wt / mu cDNA

1405 / 1405

Position of start ATG in wt / mu cDNA

302 / 302

Last intron/exon boundary

1271

Theoretical NMD boundary in CDS

919

Length of CDS

1104

Coding sequence (CDS) position

124

cDNA position

425

gDNA position

11048

Chromosomal position

3647506

Speed

0.10 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:

17:3647506G>A_7_ENST00000399306

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 64|36 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr17:3647506G>A (GRCh38)

Gene symbol

CTNS

Gene constraints

LOEUF: 1.06, LOF (oe): 0.47, misssense (oe): 0.84, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000399306.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.124G>A
g.11048G>A

AA changes

AAE:	V42I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35086888
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	167	4919	5086

Protein conservation

Species	Match	AA	Alignment
Human		42	V	V	K	L	E	N	G	S	S	T	N	V	S	L	T	L	R	P	P	L	N	A	T	L
mutated	all conserved	42	V	V	K	L	E	N	G	S	S	T	N	I	S	L	T	L	R	P	P	L	N	A	T
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)	-0.309	0.257
	0.865	0.726
(flanking)	2.52	0.865

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

17

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

17

Strand

1

Original gDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGTAA

Altered gDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGTAA

Original cDNA sequence snippet

AGAACGGCAGCTCGACCAACGTCAGCCTCACCCTGCGGCCA

Altered cDNA sequence snippet

AGAACGGCAGCTCGACCAACATCAGCCTCACCCTGCGGCCA

Wildtype AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI
TFRSKNITIL ELPDELVEAG GEECRDEISS HEAHQDGLQI SSEPPRKQTG VKHDQSPACG
NL*

Mutated AA sequence

MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NISLTLRPPL NATLVITFEI
TFRSKNITIL ELPDELVEAG GEECRDEISS HEAHQDGLQI SSEPPRKQTG VKHDQSPACG
NL*

Position of stopcodon in wt / mu CDS

369 / 369

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

123 / 123

Position of stopcodon in wt / mu cDNA

601 / 601

Position of start ATG in wt / mu cDNA

233 / 233

Last intron/exon boundary

457

Theoretical NMD boundary in CDS

174

Length of CDS

369

Coding sequence (CDS) position

124

cDNA position

356

gDNA position

11048

Chromosomal position

3647506

Speed

0.04 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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