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: ENST00000646249
Querying Taster for transcript #2: ENST00000356842
Querying Taster for transcript #3: ENST00000359629
Querying Taster for transcript #4: ENST00000642439
Querying Taster for transcript #5: ENST00000642384
Querying Taster for transcript #6: ENST00000335712
Querying Taster for transcript #7: ENST00000643716
MT speed 0.08 s - this script 2.469463 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000646249	BCL11A	Benign	3\|197	without_aae	No	Insertion	N/A	Homozygous in gnomAD
ENST00000642439	BCL11A	Benign	4\|96	5utr	No	Insertion	N/A	Homozygous in gnomAD
ENST00000356842	BCL11A	Benign	5\|95	5utr	No	Insertion	N/A	Homozygous in gnomAD
ENST00000335712	BCL11A	Benign	5\|95	5utr	No	Insertion	N/A	Homozygous in gnomAD
ENST00000642384(MANE Select)	BCL11A	Benign	6\|94	5utr	No	Insertion	N/A	Homozygous in gnomAD
ENST00000359629	BCL11A	Benign	9\|91	5utr	No	Insertion	N/A	Homozygous in gnomAD
ENST00000643716	BCL11A	Benign	11\|88	5utr	No	Insertion	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

2:60553515G>GGAGA_1_ENST00000646249

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 3|197 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.34, LOF (oe): 0.13, misssense (oe): 0.67, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000646249.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

intron

DNA changes

c.-123-123_-123-122insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	1

?

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

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIAGK DEPSSYTCTT CKQPFTSAWF LLQHAQNTHG LRIYLESEHG SPLTPRVLHT
PPFGVVPREL KMCGSFRMEA REPLSSEKI*

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

714 / 714

Last intron/exon boundary

1241

Theoretical NMD boundary in CDS

477

Length of CDS

630

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

Speed

0.02 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:

2:60553515G>GGAGA_4_ENST00000642439

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 4|96 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.34, LOF (oe): 0.13, misssense (oe): 0.67, synonymous (oe): 0.89 ? (gnomAD)

Ensembl transcript ID

ENST00000642439.1

Genbank transcript ID

NM_001405733 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.43_44insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIAGK DEPSSYTCTT CKQPFTSAWF LLQHAQNTHG LRIYLESEHG SPLTPRVLHT
PPFGVVPREL KMCGSFRMEA REPLSSEKI*

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

289 / 289

Last intron/exon boundary

816

Theoretical NMD boundary in CDS

477

Length of CDS

630

Coding sequence (CDS) position

N/A

cDNA position

43 / 44

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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:

2:60553515G>GGAGA_2_ENST00000356842

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 5|95 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.16, LOF (oe): 0.06, misssense (oe): 0.77, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000356842.9

Genbank transcript ID

NM_018014 (by similarity), NM_001405730 (by similarity), NM_001405710 (by similarity), NM_001405731 (by similarity), NM_001405726 (by similarity), NM_001405722 (by similarity), NM_001405723 (by similarity), NM_001405716 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.56_57insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIADK LLHWRGLSSP RSAHGALIPT PGMSAEYAPQ GICKDEPSSY TCTTCKQPFT
SAWFLLQHAQ NTHGLRIYLE SEHGSPLTPR VGIPSGLGAE CPSQPPLHGI HIADNNPFNL
LRIPGSVSRE ASGLAEGRFP PTPPLFSPPP RHHLDPHRIE RLGAEEMALA THHPSAFDRV
LRLNPMAMEP PAMDFSRRLR ELAGNTSSPP LSPGRPSPMQ RLLQPFQPGS KPPFLATPPL
PPLQSAPPPS QPPVKSKSCE FCGKTFKFQS NLVVHRRSHT GEKPYKCNLC DHACTQASKL
KRHMKTHMHK SSPMTVKSDD GLSTASSPEP GTSDLVGSAS SALKSVVAKF KSENDPNLIP
ENGDEEEEED DEEEEEEEEE EEEELTESER VDYGFGLSLE AARHHENSSR GAVVGVGDES
RALPDVMQGM VLSSMQHFSE AFHQVLGEKH KRGHLAEAEG HRDTCDEDSV AGESDRIDDG
TVNGRGCSPG ESASGGLSKK LLLGSPSSLS PFSKRIKLEK EFDLPPAAMP NTENVYSQWL
AGYAASRQLK DPFLSFGDSR QSPFASSSEH SSENGSLRFS TPPGELDGGI SGRSGTGSGG
STPHISGPGP GRPSSKEGRR SDTCSSHTPI RRSTQRAQDV WQFSDGSSRA LKF*

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

302 / 302

Last intron/exon boundary

2531

Theoretical NMD boundary in CDS

2179

Length of CDS

2322

Coding sequence (CDS) position

N/A

cDNA position

56 / 57

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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:

2:60553515G>GGAGA_6_ENST00000335712

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 5|95 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.13, LOF (oe): 0.04, misssense (oe): 0.70, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000335712.11

Genbank transcript ID

NM_001405712 (by similarity), NM_001405711 (by similarity), NM_001365609 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.143_144insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIAGK DEPSSYTCTT CKQPFTSAWF LLQHAQNTHG LRIYLESEHG SPLTPRVGIP
SGLGAECPSQ PPLHGIHIAD NNPFNLLRIP GSVSREASGL AEGRFPPTPP LFSPPPRHHL
DPHRIERLGA EEMALATHHP SAFDRVLRLN PMAMEPPAMD FSRRLRELAG NTSSPPLSPG
RPSPMQRLLQ PFQPGSKPPF LATPPLPPLQ SAPPPSQPPV KSKSCEFCGK TFKFQSNLVV
HRRSHTGEKP YKCNLCDHAC TQASKLKRHM KTHMHKSSPM TVKSDDGLST ASSPEPGTSD
LVGSASSALK SVVAKFKSEN DPNLIPENGD EEEEEDDEEE EEEEEEEEEE LTESERVDYG
FGLSLEAARH HENSSRGAVV GVGDESRALP DVMQGMVLSS MQHFSEAFHQ VLGEKHKRGH
LAEAEGHRDT CDEDSVAGES DRIDDGTVNG RGCSPGESAS GGLSKKLLLG SPSSLSPFSK
RIKLEKEFDL PPAAMPNTEN VYSQWLAGYA ASRQLKDPFL SFGDSRQSPF ASSSEHSSEN
GSLRFSTPPG ELDGGISGRS GTGSGGSTPH ISGPGPGRPS SKEGRRSDTC EYCGKVFKNC
SNLTVHRRSH TGERPYKCEL CNYACAQSSK LTRHMKTHGQ VGKDVYKCEI CKMPFSVYST
LEKHMKKWHS DRVLNNDIKT E*

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

389 / 389

Last intron/exon boundary

773

Theoretical NMD boundary in CDS

334

Length of CDS

2406

Coding sequence (CDS) position

N/A

cDNA position

143 / 144

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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:

2:60553515G>GGAGA_5_ENST00000642384

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 6|94 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.12, LOF (oe): 0.04, misssense (oe): 0.71, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000642384.2

Genbank transcript ID

NM_022893 (exact from MANE), NM_001405708 (by similarity), NM_001405715 (by similarity), NM_001405709 (by similarity), NM_001405728 (by similarity), NM_001405725 (by similarity), NM_001405721 (by similarity), NM_001405713 (by similarity), NM_001405729 (by similarity), NM_001405714 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.139_140insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIADK LLHWRGLSSP RSAHGALIPT PGMSAEYAPQ GICKDEPSSY TCTTCKQPFT
SAWFLLQHAQ NTHGLRIYLE SEHGSPLTPR VGIPSGLGAE CPSQPPLHGI HIADNNPFNL
LRIPGSVSRE ASGLAEGRFP PTPPLFSPPP RHHLDPHRIE RLGAEEMALA THHPSAFDRV
LRLNPMAMEP PAMDFSRRLR ELAGNTSSPP LSPGRPSPMQ RLLQPFQPGS KPPFLATPPL
PPLQSAPPPS QPPVKSKSCE FCGKTFKFQS NLVVHRRSHT GEKPYKCNLC DHACTQASKL
KRHMKTHMHK SSPMTVKSDD GLSTASSPEP GTSDLVGSAS SALKSVVAKF KSENDPNLIP
ENGDEEEEED DEEEEEEEEE EEEELTESER VDYGFGLSLE AARHHENSSR GAVVGVGDES
RALPDVMQGM VLSSMQHFSE AFHQVLGEKH KRGHLAEAEG HRDTCDEDSV AGESDRIDDG
TVNGRGCSPG ESASGGLSKK LLLGSPSSLS PFSKRIKLEK EFDLPPAAMP NTENVYSQWL
AGYAASRQLK DPFLSFGDSR QSPFASSSEH SSENGSLRFS TPPGELDGGI SGRSGTGSGG
STPHISGPGP GRPSSKEGRR SDTCEYCGKV FKNCSNLTVH RRSHTGERPY KCELCNYACA
QSSKLTRHMK THGQVGKDVY KCEICKMPFS VYSTLEKHMK KWHSDRVLNN DIKTE*

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

385 / 385

Last intron/exon boundary

871

Theoretical NMD boundary in CDS

436

Length of CDS

2508

Coding sequence (CDS) position

N/A

cDNA position

139 / 140

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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:

2:60553515G>GGAGA_3_ENST00000359629

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 9|91 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.32, LOF (oe): 0.12, misssense (oe): 0.71, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000359629.10

Genbank transcript ID

NM_138559 (by similarity), NM_001405732 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.119_120insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIADK LLHWRGLSSP RSAHGALIPT PGMSAEYAPQ GICKDEPSSY TCTTCKQPFT
SAWFLLQHAQ NTHGLRIYLE SEHGSPLTPR VLHTPPFGVV PRELKMCGSF RMEAREPLSS
EKI*

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

365 / 365

Last intron/exon boundary

994

Theoretical NMD boundary in CDS

579

Length of CDS

732

Coding sequence (CDS) position

N/A

cDNA position

119 / 120

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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:

2:60553515G>GGAGA_7_ENST00000643716

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 11|88 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:60553515_60553516insGAGA (GRCh38)

Gene symbol

BCL11A

Gene constraints

LOEUF: 0.26, LOF (oe): 0.00, misssense (oe): 0.64, synonymous (oe): 0.81 ? (gnomAD)

Ensembl transcript ID

ENST00000643716.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Insertion

Gene region

5'UTR

DNA changes

cDNA.117_118insTCTC
g.952_953insTCTC

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	rs113296120
gnomAD	homozygous (GAGA/GAGA)	heterozygous	allele carriers
	>32000	2968	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.958	1
(flanking)	1.875	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

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered gDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Original cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Altered cDNA sequence snippet

ATCTCTCTTCTCTCTCTCTCTCTCCCTCTTTTTTTTTTTTTTTT

Wildtype AA sequence

MSRRKQGKPQ HLSKREFSPE PLEAILTDDE PDHGPLGAPE GDHDLLTCGQ CQMNFPLGDI
LIFIEHKRKQ CNGSLCLEKA VDKPPSPSPI EMKKASNPVE VGIQVTPEDD DCLSTSSRGI
CPKQEHIAGK *

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

363 / 363

Last intron/exon boundary

417

Theoretical NMD boundary in CDS

4

Length of CDS

393

Coding sequence (CDS) position

N/A

cDNA position

117 / 118

gDNA position

952 / 953

Chromosomal position

60553515 / 60553516

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

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