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: ENST00000647998
Querying Taster for transcript #2: ENST00000370214
MT speed 0.03 s - this script 2.417326 s

Transcript summary:

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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
ENST00000647998	ABCD3	Deleterious	200\|0	without_aae		No				Single base exchange		N/A	Splice site lost
ENST00000370214(MANE Select)	ABCD3	Deleterious	200\|0	without_aae		No				Single base exchange		N/A	Splice site lost

MutationT@ster 2025

Variant:

1:94515203G>A_1_ENST00000647998

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Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 200|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:94515203G>A (GRCh38)

Gene symbol

ABCD3

Gene constraints

LOEUF: 0.48, LOF (oe): 0.35, misssense (oe): 0.75, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000647998.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1902+1G>A
g.96815G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.876	1
	9.998	1
(flanking)	8.014	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	96814	wt: 0.00 / mu: 0.00	-	wt: ACATCATGAG\|gtttgtattt mu: ACATCATGAG\|atttgtattt

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTTTGGAAACATCATGAGGTTTGTATTTCTTTCATTGAA

Altered gDNA sequence snippet

CTCTTTGGAAACATCATGAGATTTGTATTTCTTTCATTGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD
KVFFSRLIQI LKIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIISRNKA
LFKKPFFKFI AATPMISLVN NFLKYGLNEL KLCFRVRLTK YLYEEYLQAF TYYKMGNLDN
RIANPDQLLT QDVEKFCNSV VDLYSNLSKP FLDIVLYIFK LTSAIGAQGP ASMMAYLVVS
GLFLTRLRRP IGKMTITEQK YEGEYRYVNS RLITNSEEIA FYNGNKREKQ TVHSVFRKLV
EHLHNFILFR FSMGFIDSII AKYLATVVGY LVVSRPFLDL SHPRHLKSTH SELLEDYYQS
GRMLLRMSQA LGRIVLAGRE MTRLAGFTAR ITELMQVLKD LNHGKYERTM VSQQEKGIEG
VQVIPLIPGA GEIIIADNII KFDHVPLATP NGDVLIRDLN FEVRSGANVL ICGPNGCGKS
SLFRVLGELW PLFGGRLTKP ERGKLFYVPQ RPYMTLGTLR DQVIYPDGRE DQKRKGISDL
VLKEYLDNVQ LGHILEREGG WDSVQDWMDV LSGGEKQRMA MARLFYHKPQ FAILDECTSA
VSVDVEGYIY SHCRKVGITL FTVSHRKSLW KHHEYYLHMD GRGNYEFKQI TEDTVEFGS*

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

25 / 25

Last intron/exon boundary

1926

Theoretical NMD boundary in CDS

1851

Length of CDS

1980

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

96815

Chromosomal position

94515203

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

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MutationT@ster 2025

Variant:

1:94515203G>A_2_ENST00000370214

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Prediction:

DeleteriousPermalink

Summary:

Splice site lost

Model: without_aae
Tree vote: 200|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:94515203G>A (GRCh38)

Gene symbol

ABCD3

Gene constraints

LOEUF: 0.48, LOF (oe): 0.35, misssense (oe): 0.74, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000370214.9

Genbank transcript ID

NM_002858 (exact from MANE)

UniProt / AlphaMissense peptide

ABCD3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1902+1G>A
g.96815G>A

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

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

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	3.876	1
	9.998	1
(flanking)	8.014	1

?

Splice sites

alteration within used splice site, likely to disturb normal splicing

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Donor lost	96814	wt: 0.00 / mu: 0.00	-	wt: ACATCATGAG\|gtttgtattt mu: ACATCATGAG\|atttgtattt

Distance from splice site

1

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTTTGGAAACATCATGAGGTTTGTATTTCTTTCATTGAA

Altered gDNA sequence snippet

CTCTTTGGAAACATCATGAGATTTGTATTTCTTTCATTGAA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD
KVFFSRLIQI LKIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK
DFKRYLLNFI AAMPLISLVN NFLKYGLNEL KLCFRVRLTK YLYEEYLQAF TYYKMGNLDN
RIANPDQLLT QDVEKFCNSV VDLYSNLSKP FLDIVLYIFK LTSAIGAQGP ASMMAYLVVS
GLFLTRLRRP IGKMTITEQK YEGEYRYVNS RLITNSEEIA FYNGNKREKQ TVHSVFRKLV
EHLHNFILFR FSMGFIDSII AKYLATVVGY LVVSRPFLDL SHPRHLKSTH SELLEDYYQS
GRMLLRMSQA LGRIVLAGRE MTRLAGFTAR ITELMQVLKD LNHGKYERTM VSQQEKGIEG
VQVIPLIPGA GEIIIADNII KFDHVPLATP NGDVLIRDLN FEVRSGANVL ICGPNGCGKS
SLFRVLGELW PLFGGRLTKP ERGKLFYVPQ RPYMTLGTLR DQVIYPDGRE DQKRKGISDL
VLKEYLDNVQ LGHILEREGG WDSVQDWMDV LSGGEKQRMA MARLFYHKPQ FAILDECTSA
VSVDVEGYIY SHCRKVGITL FTVSHRKSLW KHHEYYLHMD GRGNYEFKQI TEDTVEFGS*

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

91 / 91

Last intron/exon boundary

1992

Theoretical NMD boundary in CDS

1851

Length of CDS

1980

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

96815

Chromosomal position

94515203

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