mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999976717223 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990633)
known disease mutation: rs25160 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34647675T>CN/A show variant in all transcripts IGV

HGNC symbol

GALT

Ensembl transcript ID

ENST00000378842

Genbank transcript ID

NM_000155

UniProt peptide

P07902

alteration type

single base exchange

alteration region

CDS

DNA changes

c.350T>C
cDNA.392T>C
g.9546T>C

AA changes

F117S Score: 155 explain score(s)

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

117

frameshift

known variant

Reference ID: rs111033679
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs25160 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990633)

regulatory features

H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.006	1
	4.533	1
(flanking)	0.642	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 marginally increased	9547	wt: 0.6134 / mu: 0.6412 (marginal change - not scored)	wt: CCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAGG mu: CCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAGG	tttc\|CAAG
Donor increased	9545	wt: 0.53 / mu: 0.79	wt: CCCTTTTCCAAGCAA mu: CCCTTTCCCAAGCAA	CTTT\|tcca
Donor marginally increased	9550	wt: 0.9990 / mu: 0.9991 (marginal change - not scored)	wt: TTCCAAGCAAAGTCT mu: TCCCAAGCAAAGTCT	CCAA\|gcaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

117

mutated

not conserved

117

Ptroglodytes

all identical

ENSPTRG00000020886

117

Mmulatta

all identical

ENSMMUG00000020789

117

Fcatus

all identical

ENSFCAG00000016304

117

Mmusculus

all identical

ENSMUSG00000036073

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016445

102

Drerio

all identical

ENSDARG00000069543

102

Dmelanogaster

all identical

FBgn0263200

Celegans

all identical

ZK1058.3

Xtropicalis

all conserved

ENSXETG00000013206

protein features

start (aa)	end (aa)	feature	details
184	184	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
186	186	ACT_SITE	Tele-UMP-histidine intermediate (By similarity).	might get lost (downstream of altered splice site)
202	202	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
258	259	CONFLICT	RR -> VG (in Ref. 1; AAC83409).	might get lost (downstream of altered splice site)
301	301	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
319	319	METAL	Iron (Potential).	might get lost (downstream of altered splice site)
321	321	METAL	Iron (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1140 / 1140

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

380 / 380

position of stopcodon in wt / mu cDNA

1182 / 1182

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

43 / 43

chromosome

strand

last intron/exon boundary

1102

theoretical NMD boundary in CDS

1009

length of CDS

1140

coding sequence (CDS) position

350

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

392

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

9546

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

34647675

original gDNA sequence snippet

ACCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAG

altered gDNA sequence snippet

ACCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAG

original cDNA sequence snippet

ACCCAGTGATCATCCCCTTTTCCAAGCAAAGTCTGCTCGAG

altered cDNA sequence snippet

ACCCAGTGATCATCCCCTTTCCCAAGCAAAGTCTGCTCGAG

wildtype AA sequence

MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLFQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*

mutated AA sequence

MSRSGTDPQQ RQQASEADAA AATFRANDHQ HIRYNPLQDE WVLVSAHRMK RPWQGQVEPQ
LLKTVPRHDP LNPLCPGAIR ANGEVNPQYD STFLFDNDFP ALQPDAPSPG PSDHPLSQAK
SARGVCKVMC FHPWSDVTLP LMSVPEIRAV VDAWASVTEE LGAQYPWVQI FENKGAMMGC
SNPHPHCQVW ASSFLPDIAQ REERSQQAYK SQHGEPLLME YSRQELLRKE RLVLTSEHWL
VLVPFWATWP YQTLLLPRRH VRRLPELTPA ERDDLASIMK KLLTKYDNLF ETSFPYSMGW
HGAPTGSEAG ANWNHWQLHA HYYPPLLRSA TVRKFMVGYE MLAQAQRDLT PEQAAERLRA
LPEVHYHLGQ KDRETATIA*

speed

0.32 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