MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000648911
Querying Taster for transcript #2: ENST00000278919
MT speed 0.23 s - this script 2.672319 s

Transcript summary:

Permalink

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
ENST00000278919(MANE Select)	FEZ1	Benign	64\|36	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000648911	FEZ1	Benign	71\|29	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

11:125481576A>T_2_ENST00000278919

Back to summary table

Prediction:

BenignPermalink

Summary:

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

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

Chr11:125481576A>T (GRCh38)

Gene symbol

FEZ1

Gene constraints

LOEUF: 0.66, LOF (oe): 0.41, misssense (oe): 0.82, synonymous (oe): 0.83 ? (gnomAD)

Ensembl transcript ID

ENST00000278919.8

Genbank transcript ID

NM_005103 (exact from MANE)

UniProt / AlphaMissense peptide

FEZ1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.369T>A
g.110993T>A

AA changes

AAE:	D123E	?
Score:	45

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs597570
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	26699	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		123	N	Y	I	P	S	L	S	E	D	W	R	D	P	N	I	E	A	L	N	G	N	C	S	D
mutated	all conserved	123										W	R	E	P	N	I	E	A	L	N	G	N	C	S
Ptroglodytes	all identical	123										W	R	D	P	N	I	E	A	L	N	G	N	C	S
Mmulatta	all identical	123										W	R	D	P	N	I	E	A	L	N	G	N	C	S
Fcatus	all identical	123										W	R	D	P	N	M	E	A	L	N	G	N	S	S
Mmusculus	all identical	123										W	R	D	P	N	I	E	A	L	N	G	N	S	S
Ggallus	not conserved	112									P	W	M	H	P	E	A	E	A	P	D	G	-	-	T
Trubripes	not conserved	127				S	T	-	-	-	-	W	D	S	Q	D	A	E	G	L	N	G	N	L	S
Drerio	no homologue
Dmelanogaster	not conserved	204							P	I	D	WSKSYT	R	Q	M	H	M	P	T	L	N	L	G	Q	N
Celegans	all identical	118						FGTSSICKKMAAALD	S	D	S	L	K	D	D	A	S	T	R	R	S	M	T	N	S
Xtropicalis	all identical	122										W	R	D	Q	S	L	E	S	L	N	G	N	M	S

Protein features

Start (aa)	End (aa)	Feature	Details
1	392	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.785	1
	2.299	1
(flanking)	1.937	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

11

Strand

-1

Original gDNA sequence snippet

CTCTCAGAAGACTGGAGGGATCCAAACATCGAGGCTCTGAA

Altered gDNA sequence snippet

CTCTCAGAAGACTGGAGGGAACCAAACATCGAGGCTCTGAA

Original cDNA sequence snippet

CTCTCAGAAGACTGGAGGGATCCAAACATCGAGGCTCTGAA

Altered cDNA sequence snippet

CTCTCAGAAGACTGGAGGGAACCAAACATCGAGGCTCTGAA

Wildtype AA sequence

MEAPLVSLDE EFEDLRPSCS EDPEEKPQCF YGSSPHHLED PSLSELENFS SEIISFKSME
DLVNEFDEKL NVCFRNYNAK TENLAPVKNQ LQIQEEEETL QDEEVWDALT DNYIPSLSED
WRDPNIEALN GNCSDTEIHE KEEEEFNEKS ENDSGINEEP LLTADQVIEE IEEMMQNSPD
PEEEEEVLEE EDGGETSSQA DSVLLQEMQA LTQTFNNNWS YEGLRHMSGS ELTELLDQVE
GAIRDFSEEL VQQLARRDEL EFEKEVKNSF ITVLIEVQNK QKEQRELMKK RRKEKGLSLQ
SSRIEKGNQM PLKRFSMEGI SNILQSGIRQ TFGSSGTDKQ YLNTVIPYEK KASPPSVEDL
QMLTNILFAM KEDNEKVPTL LTDYILKVLC PT*

Mutated AA sequence

MEAPLVSLDE EFEDLRPSCS EDPEEKPQCF YGSSPHHLED PSLSELENFS SEIISFKSME
DLVNEFDEKL NVCFRNYNAK TENLAPVKNQ LQIQEEEETL QDEEVWDALT DNYIPSLSED
WREPNIEALN GNCSDTEIHE KEEEEFNEKS ENDSGINEEP LLTADQVIEE IEEMMQNSPD
PEEEEEVLEE EDGGETSSQA DSVLLQEMQA LTQTFNNNWS YEGLRHMSGS ELTELLDQVE
GAIRDFSEEL VQQLARRDEL EFEKEVKNSF ITVLIEVQNK QKEQRELMKK RRKEKGLSLQ
SSRIEKGNQM PLKRFSMEGI SNILQSGIRQ TFGSSGTDKQ YLNTVIPYEK KASPPSVEDL
QMLTNILFAM KEDNEKVPTL LTDYILKVLC PT*

Position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

Position of stopcodon in wt / mu cDNA

1369 / 1369

Position of start ATG in wt / mu cDNA

191 / 191

Last intron/exon boundary

1352

Theoretical NMD boundary in CDS

1111

Length of CDS

1179

Coding sequence (CDS) position

369

cDNA position

559

gDNA position

110993

Chromosomal position

125481576

Speed

0.12 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:

11:125481576A>T_1_ENST00000648911

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 71|29 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr11:125481576A>T (GRCh38)

Gene symbol

FEZ1

Gene constraints

LOEUF: 0.66, LOF (oe): 0.41, misssense (oe): 0.82, synonymous (oe): 0.83 ? (gnomAD)

Ensembl transcript ID

ENST00000648911.1

Genbank transcript ID

UniProt / AlphaMissense peptide

FEZ1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.369T>A
g.110993T>A

AA changes

AAE:	D123E	?
Score:	45

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs597570
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	26699	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		123	N	Y	I	P	S	L	S	E	D	W	R	D	P	N	I	E	A	L	N	G	N	C	S	D
mutated	all conserved	123										W	R	E	P	N	I	E	A	L	N	G	N	C	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	392	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.785	1
	2.299	1
(flanking)	1.937	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

11

Strand

-1

Original gDNA sequence snippet

CTCTCAGAAGACTGGAGGGATCCAAACATCGAGGCTCTGAA

Altered gDNA sequence snippet

CTCTCAGAAGACTGGAGGGAACCAAACATCGAGGCTCTGAA

Original cDNA sequence snippet

CTCTCAGAAGACTGGAGGGATCCAAACATCGAGGCTCTGAA

Altered cDNA sequence snippet

CTCTCAGAAGACTGGAGGGAACCAAACATCGAGGCTCTGAA

Wildtype AA sequence

MEAPLVSLDE EFEDLRPSCS EDPEEKPQCF YGSSPHHLED PSLSELENFS SEIISFKSME
DLVNEFDEKL NVCFRNYNAK TENLAPVKNQ LQIQEEEETL QDEEVWDALT DNYIPSLSED
WRDPNIEALN GNCSDTEIHE KEEEEFNEKS ENDSGINEEP LLTADQVIEE IEEMMQNSPD
PEEEEEVLEE EDGGETSSQA DSVLLQEMQA LTQTFNNNWS YEGLRHMSGS ELTELLDQVE
GAIRDFSEEL VQQLARRDEL EFEKEVKNSF ITVLIEVQNK QKEQRELMKK RRKEKGLSLQ
SSRIEKGNQM PLKRFSMEGI SNILQSGIRQ TFGSSGTDKQ YLNTVIPYEK KASPPSVEDL
QMLTNILFAM KEDNEKVPTL LTDYILKVLC PT*

Mutated AA sequence

MEAPLVSLDE EFEDLRPSCS EDPEEKPQCF YGSSPHHLED PSLSELENFS SEIISFKSME
DLVNEFDEKL NVCFRNYNAK TENLAPVKNQ LQIQEEEETL QDEEVWDALT DNYIPSLSED
WREPNIEALN GNCSDTEIHE KEEEEFNEKS ENDSGINEEP LLTADQVIEE IEEMMQNSPD
PEEEEEVLEE EDGGETSSQA DSVLLQEMQA LTQTFNNNWS YEGLRHMSGS ELTELLDQVE
GAIRDFSEEL VQQLARRDEL EFEKEVKNSF ITVLIEVQNK QKEQRELMKK RRKEKGLSLQ
SSRIEKGNQM PLKRFSMEGI SNILQSGIRQ TFGSSGTDKQ YLNTVIPYEK KASPPSVEDL
QMLTNILFAM KEDNEKVPTL LTDYILKVLC PT*

Position of stopcodon in wt / mu CDS

1179 / 1179

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

393 / 393

Position of stopcodon in wt / mu cDNA

1530 / 1530

Position of start ATG in wt / mu cDNA

352 / 352

Last intron/exon boundary

1513

Theoretical NMD boundary in CDS

1111

Length of CDS

1179

Coding sequence (CDS) position

369

cDNA position

720

gDNA position

110993

Chromosomal position

125481576

Speed

0.11 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