mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999990404836196 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM080148)
known disease mutation: rs18369 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:233393011T>CN/A show variant in all transcripts IGV

HGNC symbol

CHRND

Ensembl transcript ID

ENST00000543200

Genbank transcript ID

N/A

UniProt peptide

Q07001

alteration type

single base exchange

alteration region

CDS

DNA changes

c.238T>C
cDNA.294T>C
g.2309T>C

AA changes

F80L Score: 22 explain score(s)

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

frameshift

known variant

Reference ID: rs121909506

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation: rs18369 (pathogenic for Lethal multiple pterygium syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.962	0.078
	4.261	0.996
(flanking)	2.569	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
Donor increased	2311	wt: 0.30 / mu: 0.45	wt: GAATTTGGAAACATC mu: GAACTTGGAAACATC	ATTT\|ggaa
Donor marginally increased	2300	wt: 0.8294 / mu: 0.8926 (marginal change - not scored)	wt: GGAATGCTGAAGAAT mu: GGAATGCTGAAGAAC	AATG\|ctga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000013040

Mmulatta

all identical

ENSMMUG00000022147

Fcatus

all identical

ENSFCAG00000005679

Mmusculus

all identical

ENSMUSG00000026251

Ggallus

all identical

ENSGALG00000007899

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000019342

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000027884

protein features

start (aa)	end (aa)	feature	details
22	245	TOPO_DOM	Extracellular (Potential).	lost
97	97	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
151	151	DISULFID	By similarity.	might get lost (downstream of altered splice site)
164	164	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
165	165	DISULFID	By similarity.	might get lost (downstream of altered splice site)
246	270	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
278	299	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
312	333	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
334	471	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
390	390	MOD_RES	Phosphotyrosine; by Tyr-kinases (By similarity).	might get lost (downstream of altered splice site)
472	490	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1509 / 1509

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

503 / 503

position of stopcodon in wt / mu cDNA

1565 / 1565

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

57 / 57

chromosome

strand

last intron/exon boundary

1383

theoretical NMD boundary in CDS

1276

length of CDS

1509

coding sequence (CDS) position

238

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

294

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

2309

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

233393011

original gDNA sequence snippet

TGAAGTGGAATGCTGAAGAATTTGGAAACATCAGTGTCCTG

altered gDNA sequence snippet

TGAAGTGGAATGCTGAAGAACTTGGAAACATCAGTGTCCTG

original cDNA sequence snippet

TGAAGTGGAATGCTGAAGAATTTGGAAACATCAGTGTCCTG

altered cDNA sequence snippet

TGAAGTGGAATGCTGAAGAACTTGGAAACATCAGTGTCCTG

wildtype AA sequence

MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLGWTD NRLKWNAEEF GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLPADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*

mutated AA sequence

MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLGWTD NRLKWNAEEL GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLPADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*

speed

0.98 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