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: ENST00000335295
Querying Taster for transcript #2: ENST00000647020
Querying Taster for transcript #3: ENST00000485743
Querying Taster for transcript #4: ENST00000380315
MT speed 0.31 s - this script 2.74268 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Known ClinVar disease mutation	Amino acid changes	Variant type	Protein length	Features at a glance
ENST00000485743	HBB	Deleterious	10\|0	complex_aae	No	Yes	E27*	Single base exchange	Strongly truncated protein, might cause NMD (-85 AA / more than 10% missing)	Amino acid sequence changed Known disease mutation: ClinVar ID 38650 (pathogenic) Truncated protein (might cause NMD)
ENST00000647020	HBB	Deleterious	10\|0	complex_aae	No	Yes	E27*	Single base exchange	NMD	Amino acid sequence changed Known disease mutation: ClinVar ID 38650 (pathogenic) NMD Protein features (might be) affected
ENST00000335295(MANE Select)	HBB	Deleterious	10\|0	complex_aae	No	Yes	E27*	Single base exchange	NMD	Amino acid sequence changed Known disease mutation: ClinVar ID 38650 (pathogenic) NMD Protein features (might be) affected

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

11:5226943C>A_3_ENST00000485743

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 38650 (pathogenic)
Truncated protein (might cause NMD)

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

Analysed issue

Analysis result

Variant

Chr11:5226943C>A (GRCh38)

Gene symbol

HBB

Gene constraints

LOEUF: 1.95, LOF (oe): 1.69, misssense (oe): 0.89, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000485743.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.79G>T
g.2453G>T

AA changes

AAE:

E27*

A28-

L29-

G30-

R31-

L32-

L33-

V34-

V35-

Y36-

P37-

W38-

T39-

Q40-

R41-

F42-

F43-

E44-

S45-

F46-

G47-

D48-

L49-

S50-

T51-

P52-

D53-

A54-

V55-

M56-

G57-

N58-

P59-

K60-

V61-

K62-

A63-

H64-

G65-

K66-

K67-

V68-

L69-

G70-

A71-

F72-

S73-

D74-

G75-

L76-

A77-

H78-

L79-

D80-

N81-

L82-

K83-

G84-

T85-

F86-

A87-

T88-

L89-

S90-

E91-

L92-

H93-

C94-

D95-

K96-

L97-

H98-

V99-

D100-

P101-

E102-

N103-

F104-

R105-

V106-

S107-

L108-

W109-

D110-

A111-

*112-

?

Score:

-

Frameshift

No

Length of protein

Strongly truncated protein, might cause NMD (-85 AA / more than 10% missing)

Pathogenic variant (ClinVar)

Hemoglobinopathy
beta Thalassemia

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		27	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y	P	W	T
mutated	no alignment	n/a
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)	5.514	0.997
	1.148	0.676
(flanking)	-0.026	0.001

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

14

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTA

Altered gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGTTGGTA

Original cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTG

Altered cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGCTGCTG

Wildtype AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRVSLWD A*

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGG*

Position of stopcodon in wt / mu CDS

336 / 81

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

112 / 27

Position of stopcodon in wt / mu cDNA

387 / 132

Position of start ATG in wt / mu cDNA

52 / 52

Last intron/exon boundary

143

Theoretical NMD boundary in CDS

41

Length of CDS

336

Coding sequence (CDS) position

79

cDNA position

130

gDNA position

2453

Chromosomal position

5226943

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:

11:5226943C>A_2_ENST00000647020

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 38650 (pathogenic)
NMD
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr11:5226943C>A (GRCh38)

Gene symbol

HBB

Gene constraints

LOEUF: 1.96, LOF (oe): 1.80, misssense (oe): 0.84, synonymous (oe): 1.30 ? (gnomAD)

Ensembl transcript ID

ENST00000647020.1

Genbank transcript ID

UniProt / AlphaMissense peptide

HBB_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.79G>T
g.2453G>T

AA changes

E27* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hemoglobinopathy
beta Thalassemia

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		27	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y	P	W	T
mutated	no alignment	n/a
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
2	147	CHAIN		lost
3	147	DOMAIN	Globin	lost
21	35	HELIX		lost
26	27	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
30	31	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
33	39	PEPTIDE		lost
33	42	PEPTIDE		lost
36	37	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
37	42	HELIX		lost
38	39	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
44	46	HELIX		lost
45	45	MOD_RES	Phosphoserine	lost
46	47	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
51	51	MOD_RES	Phosphothreonine	lost
52	57	HELIX		lost
53	54	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
57	58	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
59	75	HELIX		lost
60	60	SITE		lost
60	60	MOD_RES	N6-acetyllysine	lost
64	64	BINDING	heme b	lost
67	67	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
72	73	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
75	76	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
78	80	TURN		lost
82	95	HELIX		lost
83	83	BINDING	(2R)-2,3-bisphosphoglycerate	lost
83	83	MOD_RES	N6-acetyllysine	lost
83	83	SITE		lost
85	86	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
88	88	MOD_RES	Phosphothreonine	lost
93	93	BINDING	heme b	lost
93	94	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
94	94	MOD_RES	S-nitrosocysteine	lost
96	96	SITE		lost
102	119	HELIX		lost
105	106	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
111	112	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
120	121	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
120	122	HELIX		lost
121	121	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
123	124	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
125	143	HELIX		lost
129	130	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
141	142	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
144	144	BINDING	(2R)-2,3-bisphosphoglycerate	lost
144	146	HELIX		lost
145	145	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
145	145	MOD_RES	N6-acetyllysine	lost
145	146	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.514	0.997
	1.148	0.676
(flanking)	-0.026	0.001

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

14

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTA

Altered gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGTTGGTA

Original cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTG

Altered cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGCTGCTG

Wildtype AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH*

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGG*

Position of stopcodon in wt / mu CDS

444 / 81

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

148 / 27

Position of stopcodon in wt / mu cDNA

620 / 257

Position of start ATG in wt / mu cDNA

177 / 177

Last intron/exon boundary

491

Theoretical NMD boundary in CDS

264

Length of CDS

444

Coding sequence (CDS) position

79

cDNA position

255

gDNA position

2453

Chromosomal position

5226943

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

Back to summary table

MutationT@ster 2025

Variant:

11:5226943C>A_1_ENST00000335295

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 38650 (pathogenic)
NMD
Protein features (might be) affected

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

Analysed issue

Analysis result

Variant

Chr11:5226943C>A (GRCh38)

Gene symbol

HBB

Gene constraints

LOEUF: 1.96, LOF (oe): 1.80, misssense (oe): 0.84, synonymous (oe): 1.30 ? (gnomAD)

Ensembl transcript ID

ENST00000335295.4

Genbank transcript ID

NM_000518 (exact from MANE)

UniProt / AlphaMissense peptide

HBB_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.79G>T
g.2453G>T

AA changes

E27* Score: 6.0?

Frameshift

No

Length of protein

NMD

Pathogenic variant (ClinVar)

Hemoglobinopathy
beta Thalassemia

pathogenic

ClinVar

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		27	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y	P	W	T	Q	R	F	F	E	S	F	G	D	L	S	T	P	D	A	V	M	G	N	P	K	V	K	A	H	G	K	K	V	L	G	A	F	S	D	G	L	A	H	L	D	N	L	K	G	T	F	A	T	L	S	E	L	H	C	D	K	L	H	V	D	P	E	N	F	R	L	L	G	N	V	L	V	C	V	L	A	H	H	F	G	K	E	F	T	P	P	V	Q	A	A	Y	Q	K	V	V	A	G	V	A
mutated	no alignment	n/a
Ptroglodytes	all identical	27	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y	P	W	T	Q	R	F	F	E	S	F	G	D	L	S	T	P	D	A	V	M	G	N	P	K	V	K	A	H	G	K	K	V	L	G	A	F	S	D	G	L	A	H	L	D	N	L	K	G	T	F	A	T	L	S	E	L	H	C	D	K	L	H	V	D	P	E	N	F	R	L	L	G	N	V	L	V	C	V	L	A	H	H	F	G
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	partly conserved	26	W	E	K	M	Y	V	DAE	D	N	G	T	A	V	L	V	R	M	F	T	E	H	P	D	T	K	S	Y	F	T	H	F	K	G	M	D	S	A	E	E	M	K	Q	S	D	Q	V	R	G	H	G	K	R	V	F	T	A	I	N	D	M	V	Q	H	L	D	N	T	E	A	F	L	G	I	L	N	P	L	G	Q	K	H	A	T	Q	L	K	I	D	P	K	N	F	R	I	I	C	D	I	I	L	Q	L	M	E	E	K	F	G	G	D
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no alignment	n/a
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
2	147	CHAIN		lost
3	147	DOMAIN	Globin	lost
21	35	HELIX		lost
26	27	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
30	31	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
33	39	PEPTIDE		lost
33	42	PEPTIDE		lost
36	37	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
37	42	HELIX		lost
38	39	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
44	46	HELIX		lost
45	45	MOD_RES	Phosphoserine	lost
46	47	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
51	51	MOD_RES	Phosphothreonine	lost
52	57	HELIX		lost
53	54	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
57	58	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
59	75	HELIX		lost
60	60	SITE		lost
60	60	MOD_RES	N6-acetyllysine	lost
64	64	BINDING	heme b	lost
67	67	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
72	73	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
75	76	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
78	80	TURN		lost
82	95	HELIX		lost
83	83	BINDING	(2R)-2,3-bisphosphoglycerate	lost
83	83	MOD_RES	N6-acetyllysine	lost
83	83	SITE		lost
85	86	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
88	88	MOD_RES	Phosphothreonine	lost
93	93	BINDING	heme b	lost
93	94	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
94	94	MOD_RES	S-nitrosocysteine	lost
96	96	SITE		lost
102	119	HELIX		lost
105	106	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
111	112	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
120	121	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
120	122	HELIX		lost
121	121	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
123	124	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
125	143	HELIX		lost
129	130	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
141	142	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost
144	144	BINDING	(2R)-2,3-bisphosphoglycerate	lost
144	146	HELIX		lost
145	145	CARBOHYD	N-linked (Glc) (glycation) lysine	lost
145	145	MOD_RES	N6-acetyllysine	lost
145	146	SITE	(Microbial infection) Cleavage; by N.americanus apr- 2	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.514	0.997
	1.148	0.676
(flanking)	-0.026	0.001

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

14

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGTTGGTA

Altered gDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGTTGGTA

Original cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGGCTGCTG

Altered cDNA sequence snippet

ACGTGGATGAAGTTGGTGGTTAGGCCCTGGGCAGGCTGCTG

Wildtype AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH*

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEVGG*

Position of stopcodon in wt / mu CDS

444 / 81

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

148 / 27

Position of stopcodon in wt / mu cDNA

494 / 131

Position of start ATG in wt / mu cDNA

51 / 51

Last intron/exon boundary

365

Theoretical NMD boundary in CDS

264

Length of CDS

444

Coding sequence (CDS) position

79

cDNA position

129

gDNA position

2453

Chromosomal position

5226943

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

Problem:

1

MutationT@ster 2025

annotation problem

The chosen transcript ENST00000380315 on chromosome 11 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

Back to summary table