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 CM994594)
known disease mutation: rs2612 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:3397701A>GN/A show variant in all transcripts IGV

HGNC symbol

SPATA22

Ensembl transcript ID

ENST00000541913

Genbank transcript ID

N/A

UniProt peptide

Q8NHS9

alteration type

single base exchange

alteration region

intron

DNA changes

g.19446T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs104894550

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

known disease mutation: rs2612 (pathogenic for Spongy degeneration of central nervous system) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994594)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.374	1
	1.295	1
(flanking)	0.883	1

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

splice sites

splice site change before start ATG (at aa -23) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc marginally increased	19440	wt: 0.9432 / mu: 0.9580 (marginal change - not scored)	wt: CAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTCT mu: CAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTCT	tccc\|GGGG
Acc increased	19439	wt: 0.57 / mu: 0.67	wt: GCAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTC mu: GCAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTC	atcc\|CGGG
Acc increased	19441	wt: 0.82 / mu: 0.91	wt: AATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTCTCTA mu: AATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTCTCTA	cccg\|GGGG
Acc marginally increased	19437	wt: 0.9307 / mu: 0.9394 (marginal change - not scored)	wt: CAGCAATTTCTCCATTTTCATCCCGGGGGTAATCAACTTTC mu: CAGCAATTTCTCCATTTTCATCCCGGGGGCAATCAACTTTC	tcat\|CCCG
Donor increased	19443	wt: 0.22 / mu: 0.41	wt: CCCGGGGGTAATCAA mu: CCCGGGGGCAATCAA	CGGG\|ggta
Donor gained	19447	0.54	mu: GGGGCAATCAACTTT	GGCA\|atca

distance from splice site

19005

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
6	6	CONFLICT	N -> S (in Ref. 1; AAK51120/AAK53408/ AAK61373/AAK61374).	might get lost (downstream of altered splice site)
84	84	CONFLICT	V -> A (in Ref. 1; AAK53408/AAK61373/ AAK61374).	might get lost (downstream of altered splice site)
279	279	MOD_RES	Phosphotyrosine.	might get lost (downstream of altered splice site)
280	280	MOD_RES	Phosphotyrosine.	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

515 / 515

chromosome

strand

-1

last intron/exon boundary

1367

theoretical NMD boundary in CDS

802

length of CDS

1044

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)

19446

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

3397701

original gDNA sequence snippet

CTCCATTTTCATCCCGGGGGTAATCAACTTTCTCTATAATT

altered gDNA sequence snippet

CTCCATTTTCATCCCGGGGGCAATCAACTTTCTCTATAATT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MKRSLNENSA RSTAGCLPVP LFNQKKRNRQ PLTSNPLKDD SDWAWEAVNP ELAPVMKTVD
TGQIPHSVSR PLRSQDSVFN SIQSNTGRSQ GGWSYRDGNK NTSLKTWNKN DFKPQCKRTN
LVANDGKNSC PVSSGAQQQK QLRIPEPPNL SRNKETELLR QTHSSKISGC TMRGLDKNSA
LQTLKPNFQQ NQYKKQMLDD IPEDNTLKET SLYQLQFKEK ASSLRIISAV IESMKYWREH
AQKTVLLFEV LAVLDSAVTP GPYYSKTFLM RDGKNTLPCV FYEIDRELPR LIRGRVHRCV
GNYDQKKNIF QCVSVRPASV SEQKTFQAFV KIADVEMQYY INVMNET*

mutated AA sequence

N/A

speed

0.91 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