mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM973226)
known disease mutation at this position (HGMD CS951419)
known disease mutation: rs25146 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:34647526A>GN/A show variant in all transcripts IGV

HGNC symbol

GALT

Ensembl transcript ID

ENST00000450095

Genbank transcript ID

NM_001258332

UniProt peptide

P07902

alteration type

single base exchange

alteration region

intron

DNA changes

g.9397A>G

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs111033669

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

known disease mutation: rs25146 (pathogenic for Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CS951419)

known disease mutation at this position, please check HGMD for details (HGMD ID CS951419)
known disease mutation at this position, please check HGMD for details (HGMD ID CM973226)

known disease mutation at this position, please check HGMD for details (HGMD ID CS951419)
known disease mutation at this position, please check HGMD for details (HGMD ID CM973226)
known disease mutation at this position, please check HGMD for details (HGMD ID CS951419)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
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
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.455	1
	2.062	1
(flanking)	0.067	0.997

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	9389	wt: 0.20 / mu: 0.44	wt: CAGTACGATAGCACCTTCCTGTTTGACAACGACTTCCCAGC mu: CAGTACGATAGCACCTTCCTGTTTGACAGCGACTTCCCAGC	cctg\|TTTG
Acc increased	9396	wt: 0.25 / mu: 0.56	wt: ATAGCACCTTCCTGTTTGACAACGACTTCCCAGCTCTGCAG mu: ATAGCACCTTCCTGTTTGACAGCGACTTCCCAGCTCTGCAG	gaca\|ACGA
Acc marginally increased	9392	wt: 0.7480 / mu: 0.7502 (marginal change - not scored)	wt: TACGATAGCACCTTCCTGTTTGACAACGACTTCCCAGCTCT mu: TACGATAGCACCTTCCTGTTTGACAGCGACTTCCCAGCTCT	gttt\|GACA
Acc increased	9394	wt: 0.23 / mu: 0.28	wt: CGATAGCACCTTCCTGTTTGACAACGACTTCCCAGCTCTGC mu: CGATAGCACCTTCCTGTTTGACAGCGACTTCCCAGCTCTGC	ttga\|CAAC
Acc gained	9393	0.36	mu: ACGATAGCACCTTCCTGTTTGACAGCGACTTCCCAGCTCTG	tttg\|ACAG
Donor gained	9396	0.98	mu: TTGACAGCGACTTCC	GACA\|gcga

distance from splice site

271

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
75	75	METAL	Zinc (Potential).	might get lost (downstream of altered splice site)
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

N/A

AA sequence altered

N/A

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

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

272 / 272

chromosome

strand

last intron/exon boundary

1004

theoretical NMD boundary in CDS

682

length of CDS

813

coding sequence (CDS) position

N/A

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

N/A

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

9397

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

34647526

original gDNA sequence snippet

TAGCACCTTCCTGTTTGACAACGACTTCCCAGCTCTGCAGC

altered gDNA sequence snippet

TAGCACCTTCCTGTTTGACAGCGACTTCCCAGCTCTGCAGC

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MTLSTLCVLG PSEPTESKVM CFHPWSDVTL PLMSVPEIRA VVDAWASVTE ELGAQYPWVQ
IFENKGAMMG CSNPHPHCQV WASSFLPDIA QREERSQQAY KSQHGEPLLM EYSRQELLRK
ERLVLTSEHW LVLVPFWATW PYQTLLLPRR HVRRLPELTP AERDDLASIM KKLLTKYDNL
FETSFPYSMG WHGAPTGSEA GANWNHWQLH AHYYPPLLRS ATVRKFMVGY EMLAQAQRDL
TPEQAAERLR ALPEVHYHLG QKDRETATIA *

mutated AA sequence

N/A

speed

0.99 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