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 CM051509)
known disease mutation: rs6092 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:10877529C>TN/A show variant in all transcripts IGV

HGNC symbol

SYCP2L

Ensembl transcript ID

ENST00000543878

Genbank transcript ID

N/A

UniProt peptide

Q5T4T6

alteration type

single base exchange

alteration region

intron

DNA changes

g.129503C>T

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs104893960

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

known disease mutation: rs6092 (pathogenic for Hypoparathyroidism, familial isolated, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051509)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	6.186	1
	6.186	1
(flanking)	-0.318	0.868

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

splice sites

splice site change before start ATG (at aa -155) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor increased	129504	wt: 0.58 / mu: 0.70	wt: CAGCCGCTCAGGTGA mu: CAGCTGCTCAGGTGA	GCCG\|ctca

distance from splice site

14217

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
214	214	CONFLICT	M -> V (in Ref. 1; CAL25570).	might get lost (downstream of altered splice site)
276	276	CONFLICT	R -> I (in Ref. 4; AAH12225).	might get lost (downstream of altered splice site)
314	314	CONFLICT	K -> E (in Ref. 1; CAL25570).	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

701 / 701

chromosome

strand

last intron/exon boundary

1536

theoretical NMD boundary in CDS

785

length of CDS

867

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)

129503

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

10877529

original gDNA sequence snippet

GGTGTTGCGCATGGCCCAGCCGCTCAGGTGACGCTGTGCCT

altered gDNA sequence snippet

GGTGTTGCGCATGGCCCAGCTGCTCAGGTGACGCTGTGCCT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MLDSFLLSLG FLVTEKTVNH LLQQEGLKTF NCILHAVPRE ERKKFPLSEG MCHLMKDLAR
TLLTVGDYDQ QVAISEALCR LTIKKSRDEL VHKWFDDEVI AEAFKEIKDR EFETDSRRFL
NHLNNRLGDQ RRVYSFPCIA AFADEHEMRK PADEKLEKFW IDFNLGSQSV TFYIDNAENT
LWDSVTLPKE AVMNFSITET EKIKIFIIYL KKPMIISYKE VMKIEIHFDL QFNISQVSIQ
ALGEDKQMLP DQTKISSELF SKSDKEDRES PSGLERETEV SLQKTSLL*

mutated AA sequence

N/A

speed

0.75 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