mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999999926684 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM014567)
known disease mutation: rs4367 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:55318045T>GN/A show variant in all transcripts IGV

HGNC symbol

DHCR24

Ensembl transcript ID

ENST00000537443

Genbank transcript ID

N/A

UniProt peptide

Q15392

alteration type

single base exchange

alteration region

CDS

DNA changes

c.764A>C
cDNA.829A>C
g.34847A>C

AA changes

Y255S Score: 144 explain score(s)

position(s) of altered AA
if AA alteration in CDS

255

frameshift

known variant

Reference ID: rs28939092
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs4367 (pathogenic for Desmosterolosis) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)

known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)
known disease mutation at this position, please check HGMD for details (HGMD ID CM014567)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.422	0.923
	5.007	1
(flanking)	5.007	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc increased	34839	wt: 0.70 / mu: 0.77	wt: CTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCTA mu: CTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCTA	ccag\|ATGC
Acc increased	34838	wt: 0.71 / mu: 0.82	wt: TCTCTGCCTCTGCAGCTTCCAGATGCTGTATGCCGACTGCT mu: TCTCTGCCTCTGCAGCTTCCAGATGCTGTCTGCCGACTGCT	tcca\|GATG
Acc marginally increased	34848	wt: 0.6335 / mu: 0.6721 (marginal change - not scored)	wt: TGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACCG mu: TGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCG	gtat\|GCCG
Acc gained	34852	0.43	mu: GCTTCCAGATGCTGTCTGCCGACTGCTACATGAACCGGGAG	gccg\|ACTG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

255

mutated

not conserved

255

Ptroglodytes

all identical

ENSPTRG00000000779

471

Mmulatta

all identical

ENSMMUG00000021577

471

Fcatus

all identical

ENSFCAG00000003989

394

Mmusculus

all identical

ENSMUSG00000034926

471

Ggallus

all identical

ENSGALG00000010798

471

Trubripes

all identical

ENSTRUG00000016297

474

Drerio

all identical

ENSDARG00000013236

471

Dmelanogaster

no homologue

Celegans

all identical

F52H2.6

480

Xtropicalis

all identical

ENSXETG00000020010

471

protein features

start (aa)	end (aa)	feature	details
53	516	TOPO_DOM	Cytoplasmic (Potential).	lost
383	384	SITE	Cleavage; by caspase (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

903 / 903

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

301 / 301

position of stopcodon in wt / mu cDNA

968 / 968

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

66 / 66

chromosome

strand

-1

last intron/exon boundary

815

theoretical NMD boundary in CDS

699

length of CDS

903

coding sequence (CDS) position

764

cDNA position
(for ins/del: last normal base / first normal base)

829

gDNA position
(for ins/del: last normal base / first normal base)

34847

chromosomal position
(for ins/del: last normal base / first normal base)

55318045

original gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered gDNA sequence snippet

CTGCAGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

original cDNA sequence snippet

GCATGGCTTCCAGATGCTGTATGCCGACTGCTACATGAACC

altered cDNA sequence snippet

GCATGGCTTCCAGATGCTGTCTGCCGACTGCTACATGAACC

wildtype AA sequence

MGTGIESSSH KYGLFQHICT AYELVLADGS FVRCTPSENS DLFYAVPWSC GTLGFLVAAE
IRIIPAKKYV KLRFEPVRGL EAICAKFTHE SQRQENHFVE GLLYSLDEAV IMTGVMTDEA
EPSKDIIPFG NNPIFRYLFG WMVPPKISLL KLTQGETLRK LYEQHHVVQD MLVPMKCLQQ
ALHTFQNDIH VYPIWLCPFI LPSQPGLVHP KGNEAELYID IGAYGEPRVK HFEARSCMRQ
LEKFVRSVHG FQMLYADCYM NREEFWEMFD GSLYHKLREK LGCQDAFPEV YDKICKAARH
*

mutated AA sequence

MGTGIESSSH KYGLFQHICT AYELVLADGS FVRCTPSENS DLFYAVPWSC GTLGFLVAAE
IRIIPAKKYV KLRFEPVRGL EAICAKFTHE SQRQENHFVE GLLYSLDEAV IMTGVMTDEA
EPSKDIIPFG NNPIFRYLFG WMVPPKISLL KLTQGETLRK LYEQHHVVQD MLVPMKCLQQ
ALHTFQNDIH VYPIWLCPFI LPSQPGLVHP KGNEAELYID IGAYGEPRVK HFEARSCMRQ
LEKFVRSVHG FQMLSADCYM NREEFWEMFD GSLYHKLREK LGCQDAFPEV YDKICKAARH
*

speed

0.84 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project