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: ENST00000333371
Querying Taster for transcript #2: ENST00000535906
MT speed 0.04 s - this script 2.423435 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
ENST00000333371(MANE Select)	VPS33B	Benign	2\|198	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000535906	VPS33B	Benign	4\|196	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

15:91002014C>T_1_ENST00000333371

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 2|198 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr15:91002014C>T (GRCh38)

Gene symbol

VPS33B

Gene constraints

LOEUF: 0.97, LOF (oe): 0.81, misssense (oe): 0.89, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000333371.8

Genbank transcript ID

NM_018668 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1405+36G>A
g.20590G>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

dbSNP ID	rs116787959
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	500	8876	9376

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-2.13	0
	-1.54	0
(flanking)	-1.814	0

?

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

15

Strand

-1

Original gDNA sequence snippet

AAGTGACCCCTGCTCCAGCTGTTGTCCTGACTTCTCTCAAC

Altered gDNA sequence snippet

AAGTGACCCCTGCTCCAGCTATTGTCCTGACTTCTCTCAAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAFPHRPDAP ELPDFSMLKR LARDQLIYLL EQLPGKKDLF IEADLMSPLD RIANVSILKQ
HEVDKLYKVE NKPALSSNEQ LCFLVRPRIK NMRYIASLVN ADKLAGRTRK YKVIFSPQKF
YACEMVLEEE GIYGDVSCDE WAFSLLPLDV DLLSMELPEF FRDYFLEGDQ RWINTVAQAL
HLLSTLYGPF PNCYGIGRCA KMAYELWRNL EEEEDGETKG RRPEIGHIFL LDRDVDFVTA
LCSQVVYEGL VDDTFRIKCG SVDFGPEVTS SDKSLKVLLN AEDKVFNEIR NEHFSNVFGF
LSQKARNLQA QYDRRRGMDI KQMKNFVSQE LKGLKQEHRL LSLHIGACES IMKKKTKQDF
QELIKTEHAL LEGFNIREST SYIEEHIDRQ VSPIESLRLM CLLSITENGL IPKDYRSLKT
QYLQSYGPEH LLTFSNLRRA GLLTEQAPGD TLTAVESKVS KLVTDKAAGK ITDAFSSLAK
RSNFRAISKK LNLIPRVDGE YDLKVPRDMA YVFGGAYVPL SCRIIEQVLE RRSWQGLDEV
VRLLNCSDFA FTDMTKEDKA SSESLRLILV VFLGGCTFSE ISALRFLGRE KGYRFIFLTT
AVTNSARLME AMSEVKA*

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

346 / 346

Last intron/exon boundary

2119

Theoretical NMD boundary in CDS

1723

Length of CDS

1854

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

20590

Chromosomal position

91002014

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:

15:91002014C>T_2_ENST00000535906

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 4|196 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr15:91002014C>T (GRCh38)

Gene symbol

VPS33B

Gene constraints

LOEUF: 0.98, LOF (oe): 0.81, misssense (oe): 0.88, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000535906.1

Genbank transcript ID

NM_001289148 (by similarity), NM_001289149 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1324+36G>A
g.20590G>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

dbSNP ID	rs116787959
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	500	8876	9376

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-2.13	0
	-1.54	0
(flanking)	-1.814	0

?

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

15

Strand

-1

Original gDNA sequence snippet

AAGTGACCCCTGCTCCAGCTGTTGTCCTGACTTCTCTCAAC

Altered gDNA sequence snippet

AAGTGACCCCTGCTCCAGCTATTGTCCTGACTTCTCTCAAC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAFPHRPDAP ELPDFSMLKR LARDQLIYLL EQQHEVDKLY KVENKPALSS NEQLCFLVRP
RIKNMRYIAS LVNADKLAGR TRKYKVIFSP QKFYACEMVL EEEGIYGDVS CDEWAFSLLP
LDVDLLSMEL PEFFRDYFLE GDQRWINTVA QALHLLSTLY GPFPNCYGIG RCAKMAYELW
RNLEEEEDGE TKGRRPEIGH IFLLDRDVDF VTALCSQVVY EGLVDDTFRI KCGSVDFGPE
VTSSDKSLKV LLNAEDKVFN EIRNEHFSNV FGFLSQKARN LQAQYDRRRG MDIKQMKNFV
SQELKGLKQE HRLLSLHIGA CESIMKKKTK QDFQELIKTE HALLEGFNIR ESTSYIEEHI
DRQVSPIESL RLMCLLSITE NGLIPKDYRS LKTQYLQSYG PEHLLTFSNL RRAGLLTEQA
PGDTLTAVES KVSKLVTDKA AGKITDAFSS LAKRSNFRAI SKKLNLIPRV DGEYDLKVPR
DMAYVFGGAY VPLSCRIIEQ VLERRSWQGL DEVVRLLNCS DFAFTDMTKE DKASSESLRL
ILVVFLGGCT FSEISALRFL GREKGYRFIF LTTAVTNSAR LMEAMSEVKA *

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

348 / 348

Last intron/exon boundary

2040

Theoretical NMD boundary in CDS

1642

Length of CDS

1773

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

20590

Chromosomal position

91002014

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