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: ENST00000335295
Querying Taster for transcript #2: ENST00000647020
Querying Taster for transcript #3: ENST00000485743
Querying Taster for transcript #4: ENST00000380315
MT speed 0.21 s - this script 2.599525 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Known ClinVar disease mutation	Variant type	Protein length	Features at a glance
ENST00000335295(MANE Select)	HBB	Deleterious	87\|13	simple_aae	No	Yes	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Known disease mutation: ClinVar ID 15166 (pathogenic) Protein features (might be) affected
ENST00000485743	HBB	Deleterious	98\|2	simple_aae	No	Yes	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Known disease mutation: ClinVar ID 15166 (pathogenic)
ENST00000647020	HBB	Deleterious	98\|2	simple_aae	No	Yes	Deletion	Deletion of 1 or 2 AA	Amino acid sequence changed Known disease mutation: ClinVar ID 15166 (pathogenic) Protein features (might be) affected

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

11:5226948CCAA>C_1_ENST00000335295

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 15166 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 87|13 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:5226949_5226951delCAA (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

Deletion

Gene region

CDS

DNA changes

c.71_73delTTG
g.2445_2447delTTG

AA changes

deletion of 1 or 2 AA

AAE:	V24-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Hemoglobinopathy

pathogenic

ClinVar

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		24	T	A	L	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y
mutated	not conserved	24	T	A	L	W	G	K	V	N	V	D	E	-	G	G	E	A	L	G	R	L	L	V	V
Ptroglodytes	all identical	24	T	A	L	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	not conserved	23	R	G	A	W	E	K	M	Y	V	DAE	D	N	G	T	A	V	L	V	R	M	F	T	E
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

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.147	1
	7.147	1
	0.067	0.011
	1.191	0.006
(flanking)	-0.049	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered gDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Original cDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered cDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Wildtype AA sequence

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

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH*

Position of stopcodon in wt / mu CDS

444 / 441

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

148 / 147

Position of stopcodon in wt / mu cDNA

494 / 491

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

70 / 74

cDNA position

120 / 124

gDNA position

2444 / 2448

Chromosomal position

5226948 / 5226952

Speed

0.08 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:

11:5226948CCAA>C_3_ENST00000485743

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 15166 (pathogenic)

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:5226949_5226951delCAA (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

Deletion

Gene region

CDS

DNA changes

c.71_73delTTG
g.2445_2447delTTG

AA changes

deletion of 1 or 2 AA

AAE:	V24-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Hemoglobinopathy

pathogenic

ClinVar

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		24	T	A	L	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y
mutated	not conserved	24	T	A	L	W	G	K	V	N	V	D	E	-	G	G	E	A	L	G	R	L	L	V	V
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)	7.147	1
	7.147	1
	0.067	0.011
	1.191	0.006
(flanking)	-0.049	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered gDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Original cDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered cDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Wildtype AA sequence

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

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRVSLWDA *

Position of stopcodon in wt / mu CDS

336 / 333

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

112 / 111

Position of stopcodon in wt / mu cDNA

387 / 384

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

70 / 74

cDNA position

121 / 125

gDNA position

2444 / 2448

Chromosomal position

5226948 / 5226952

Speed

0.06 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:

11:5226948CCAA>C_2_ENST00000647020

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 15166 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 98|2 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr11:5226949_5226951delCAA (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

Deletion

Gene region

CDS

DNA changes

c.71_73delTTG
g.2445_2447delTTG

AA changes

deletion of 1 or 2 AA

AAE:	V24-	?
Score:	-

Frameshift

No

Length of protein

Deletion of 1 or 2 AA

Pathogenic variant (ClinVar)

Hemoglobinopathy

pathogenic

ClinVar

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		24	T	A	L	W	G	K	V	N	V	D	E	V	G	G	E	A	L	G	R	L	L	V	V	Y
mutated	not conserved	24	T	A	L	W	G	K	V	N	V	D	E	-	G	G	E	A	L	G	R	L	L	V	V
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

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.147	1
	7.147	1
	0.067	0.011
	1.191	0.006
(flanking)	-0.049	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

20

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

11

Strand

-1

Original gDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered gDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Original cDNA sequence snippet

CAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGCAGG

Altered cDNA sequence snippet

CAAGGTGAACGTGGATGAAGGTGGTGAGGCCCTGGGCAGG

Wildtype AA sequence

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

Mutated AA sequence

MVHLTPEEKS AVTALWGKVN VDEGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH*

Position of stopcodon in wt / mu CDS

444 / 441

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

148 / 147

Position of stopcodon in wt / mu cDNA

620 / 617

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

70 / 74

cDNA position

246 / 250

gDNA position

2444 / 2448

Chromosomal position

5226948 / 5226952

Speed

0.07 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