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: ENST00000295911
Querying Taster for transcript #2: ENST00000327047
Querying Taster for transcript #3: ENST00000328863
MT speed 0.91 s - this script 3.325986 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
ENST00000295911	CLRN1	Undetermined	50\|50	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000328863	CLRN1	Deleterious	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000327047(MANE Select)	CLRN1	Benign	39\|61	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

3:150928079T>A_1_ENST00000295911

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Prediction:

UndeterminedPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 50|50 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:150928079T>A (GRCh38)

Gene symbol

CLRN1

Gene constraints

LOEUF: 1.28, LOF (oe): 0.79, misssense (oe): 1.01, synonymous (oe): 0.81 ? (gnomAD)

Ensembl transcript ID

ENST00000295911.6

Genbank transcript ID

NM_052995 (by similarity)

UniProt / AlphaMissense peptide

CLRN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.328A>T
g.44649A>T

AA changes

AAE:	T110S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		110	T	Y	V	Y	K	T	Q	S	E	K	Y	T	T	S	F	W	L	T	K	G	H	S	*
mutated	all conserved	110	T	Y	V	Y	K	T	Q	S	E	K	Y	S	T	S	F	W	L	T	K	G	H	S
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
1	232	CHAIN		lost
101	121	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.199	1
	0.851	0.964
(flanking)	0.08	0.939

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

15

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

-1

Original gDNA sequence snippet

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGGTCATT

Altered gDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGGTCATT

Original cDNA sequence snippet

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGCTGACT

Altered cDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGCTGACT

Wildtype AA sequence

MQALQQQPVF PDLLKAIPVS IHVNVILFSA ILIVLTMVGT AFFMYNAFGK PFETLHGPLG
LYLLSFISGS CGCLVMILFA SEVKIHHLSE KIANYKEGTY VYKTQSEKYT TSFWLTKGHS
*

Mutated AA sequence

MQALQQQPVF PDLLKAIPVS IHVNVILFSA ILIVLTMVGT AFFMYNAFGK PFETLHGPLG
LYLLSFISGS CGCLVMILFA SEVKIHHLSE KIANYKEGTY VYKTQSEKYS TSFWLTKGHS
*

Position of stopcodon in wt / mu CDS

363 / 363

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

121 / 121

Position of stopcodon in wt / mu cDNA

755 / 755

Position of start ATG in wt / mu cDNA

393 / 393

Last intron/exon boundary

734

Theoretical NMD boundary in CDS

291

Length of CDS

363

Coding sequence (CDS) position

328

cDNA position

720

gDNA position

44649

Chromosomal position

150928079

Speed

0.28 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:

3:150928079T>A_3_ENST00000328863

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 51|49 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:150928079T>A (GRCh38)

Gene symbol

CLRN1

Gene constraints

LOEUF: 1.19, LOF (oe): 0.81, misssense (oe): 1.05, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000328863.8

Genbank transcript ID

NM_001195794 (by similarity)

UniProt / AlphaMissense peptide

CLRN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.595A>T
g.44649A>T

AA changes

AAE:	T199S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		199	T	Y	V	Y	K	T	Q	S	E	K	Y	T	T	S	F	W	V	I	F	F	C	F	F	V
mutated	all conserved	199	T	Y	V	Y	K	T	Q	S	E	K	Y	S	T	S	F	W	V	I	F	F	C	F	F
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
1	232	CHAIN		lost
186	206	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.199	1
	0.851	0.964
(flanking)	0.08	0.939

?

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

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGGTCATT

Altered gDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGGTCATT

Original cDNA sequence snippet

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGGTCATT

Altered cDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGGTCATT

Wildtype AA sequence

MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM
YNAFGKPFET LHGPLGLYLL SFISVALWLP ATRHQAQGSC GCLVMILFAS EVKIHHLSEK
IANYKEGTYV YKTQSEKYTT SFWVIFFCFF VHFLNGLLIR LAGFQFPFAK SKDAETTNVA
ADLMY*

Mutated AA sequence

MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM
YNAFGKPFET LHGPLGLYLL SFISVALWLP ATRHQAQGSC GCLVMILFAS EVKIHHLSEK
IANYKEGTYV YKTQSEKYST SFWVIFFCFF VHFLNGLLIR LAGFQFPFAK SKDAETTNVA
ADLMY*

Position of stopcodon in wt / mu CDS

738 / 738

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

246 / 246

Position of stopcodon in wt / mu cDNA

738 / 738

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

472

Theoretical NMD boundary in CDS

421

Length of CDS

738

Coding sequence (CDS) position

595

cDNA position

595

gDNA position

44649

Chromosomal position

150928079

Speed

0.31 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:

3:150928079T>A_2_ENST00000327047

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 39|61 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:150928079T>A (GRCh38)

Gene symbol

CLRN1

Gene constraints

LOEUF: 1.17, LOF (oe): 0.76, misssense (oe): 1.06, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000327047.6

Genbank transcript ID

NM_174878 (exact from MANE)

UniProt / AlphaMissense peptide

CLRN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.556A>T
g.44649A>T

AA changes

AAE:	T186S	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		186	T	Y	V	Y	K	T	Q	S	E	K	Y	T	T	S	F	W	V	I	F	F	C	F	F	V
mutated	all conserved	186							Q	S	E	K	Y	S	T	S	F	W	V	I	F	F	C	F	F
Ptroglodytes	all identical	199	T	Y	V	Y	K	T	Q	S	E	K	Y	T	T	S	F	W	V	V	F	F	C	F	F
Mmulatta	all identical	199	T	Y	V	Y	K	T	Q	S	E	K	Y	T	T	S	F	W	V	I	F	I	C	F	F
Fcatus	all identical	186							Q	S	E	K	Y	T	A	S	F	W	V	V	F	I	C	F	F
Mmusculus	all identical	204	T	Y	A	Y	R	T	Q	N	E	N	Y	T	T	S	F	W	V	V	F	I	C	F	F
Ggallus	not conserved	186							H	S	E	R	F	A	D	S	F	W	I	I	L	S	C	S	L
Trubripes	not conserved	186							Y	R	E	Q	Y	D	R	C	F	W	L	F	F	L	I	F	L
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	not conserved	186							H	S	E	Q	F	Q	T	S	Y	W	I	I	L	V	C	T	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	232	CHAIN		lost
186	206	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.199	1
	0.851	0.964
(flanking)	0.08	0.939

?

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

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGGTCATT

Altered gDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGGTCATT

Original cDNA sequence snippet

AAACGCAAAGTGAAAAATATACCACCTCATTCTGGGTCATT

Altered cDNA sequence snippet

AAACGCAAAGTGAAAAATATTCCACCTCATTCTGGGTCATT

Wildtype AA sequence

MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM
YNAFGKPFET LHGPLGLYLL SFISGSCGCL VMILFASEVK IHHLSEKIAN YKEGTYVYKT
QSEKYTTSFW VIFFCFFVHF LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY*

Mutated AA sequence

MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM
YNAFGKPFET LHGPLGLYLL SFISGSCGCL VMILFASEVK IHHLSEKIAN YKEGTYVYKT
QSEKYSTSFW VIFFCFFVHF LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY*

Position of stopcodon in wt / mu CDS

699 / 699

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

233 / 233

Position of stopcodon in wt / mu cDNA

718 / 718

Position of start ATG in wt / mu cDNA

20 / 20

Last intron/exon boundary

452

Theoretical NMD boundary in CDS

382

Length of CDS

699

Coding sequence (CDS) position

556

cDNA position

575

gDNA position

44649

Chromosomal position

150928079

Speed

0.32 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