mutation t@sting

Prediction

disease causing

Model: simple_aae, prob: 0.999999970191567 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051508)
known disease mutation: rs6091 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:10877576C>AN/A show variant in all transcripts IGV

HGNC symbol

GCM2

Ensembl transcript ID

ENST00000379491

Genbank transcript ID

NM_004752

UniProt peptide

O75603

alteration type

single base exchange

alteration region

CDS

DNA changes

c.140G>T
cDNA.288G>T
g.4599G>T

AA changes

R47L Score: 102 explain score(s)

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

frameshift

known variant

Reference ID: rs104893959

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

known disease mutation: rs6091 (pathogenic for Hypoparathyroidism, familial isolated, 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051508)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.657	1
	3.067	1
(flanking)	2.89	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 increased	4603	wt: 0.29 / mu: 0.76	wt: CCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATGAGAA mu: CCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAA	cttc\|ATCT
Acc increased	4607	wt: 0.85 / mu: 0.97	wt: ACGGCTATGTGCGCTTCATCTACAGCAGCGATGAGAAGAAG mu: ACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAG	atct\|ACAG
Acc increased	4609	wt: 0.70 / mu: 0.88	wt: GGCTATGTGCGCTTCATCTACAGCAGCGATGAGAAGAAGGC mu: GGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAGGC	ctac\|AGCA
Acc gained	4610	0.32	mu: GCTATGTGCTCTTCATCTACAGCAGCGATGAGAAGAAGGCA	taca\|GCAG
Acc gained	4604	0.51	mu: CTGACGGCTATGTGCTCTTCATCTACAGCAGCGATGAGAAG	ttca\|TCTA

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

ENSPTRG00000017724

Mmulatta

all identical

ENSMMUG00000007719

Fcatus

all identical

ENSFCAG00000001608

Mmusculus

all identical

ENSMUSG00000021362

Ggallus

all identical

ENSGALG00000012768

Trubripes

no homologue

Drerio

all identical

ENSDARG00000045413

Dmelanogaster

all identical

FBgn0014179

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001068

protein features

start (aa)	end (aa)	feature	details
19	174	DNA_BIND	GCM.	lost
81	81	METAL	Zinc 1 (By similarity).	might get lost (downstream of altered splice site)
87	87	METAL	Zinc 2 (By similarity).	might get lost (downstream of altered splice site)
91	91	METAL	Zinc 2 (By similarity).	might get lost (downstream of altered splice site)
118	118	METAL	Zinc 2 (By similarity).	might get lost (downstream of altered splice site)
121	121	METAL	Zinc 2 (By similarity).	might get lost (downstream of altered splice site)
130	130	METAL	Zinc 1 (By similarity).	might get lost (downstream of altered splice site)
157	157	METAL	Zinc 1 (By similarity).	might get lost (downstream of altered splice site)
159	159	METAL	Zinc 1 (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1521 / 1521

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

507 / 507

position of stopcodon in wt / mu cDNA

1669 / 1669

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

149 / 149

chromosome

strand

-1

last intron/exon boundary

731

theoretical NMD boundary in CDS

532

length of CDS

1521

coding sequence (CDS) position

140

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

288

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

4599

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

10877576

original gDNA sequence snippet

GTGGCCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATG

altered gDNA sequence snippet

GTGGCCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATG

original cDNA sequence snippet

GTGGCCTGACGGCTATGTGCGCTTCATCTACAGCAGCGATG

altered cDNA sequence snippet

GTGGCCTGACGGCTATGTGCTCTTCATCTACAGCAGCGATG

wildtype AA sequence

MPAAAVQEAV GVCSYGMQLS WDINDPQMPQ ELALFDQFRE WPDGYVRFIY SSDEKKAQRH
LSGWAMRNTN NHNGHILKKS CLGVVVCTQA CTLPDGSRLQ LRPAICDKAR LKQQKKACPN
CHSALELIPC RGHSGYPVTN FWRLDGNAIF FQAKGVHDHP RPESKSETEA RRSAIKRQMA
SFYQPQKKRI RESEAEENQD SSGHFSNIPP LENPEDFDIV TETSFPIPGQ PCPSFPKSDV
YKATCDLATF QGDKMPPFQK YSSPRIYLPR PPCSYELANP GYTNSSPYPT LYKDSTSIPN
DTDWVHLNTL QCNVNSYSSY ERSFDFTNKQ HGWKPALGKP SLVERTNHGQ FQAMATRPYY
NPELPCRYLT TPPPGAPALQ TVITTTTKVS YQAYQPPAMK YSDSVREVKS LSSCNYAPED
TGMSVYPEPW GPPVTVTRAA SPSGPPPMKI AGDCRAIRPT VAIPHEPVSS RTDEAETWDV
CLSGLGSAVS YSDRVGPFFT YNNEDF*

mutated AA sequence

MPAAAVQEAV GVCSYGMQLS WDINDPQMPQ ELALFDQFRE WPDGYVLFIY SSDEKKAQRH
LSGWAMRNTN NHNGHILKKS CLGVVVCTQA CTLPDGSRLQ LRPAICDKAR LKQQKKACPN
CHSALELIPC RGHSGYPVTN FWRLDGNAIF FQAKGVHDHP RPESKSETEA RRSAIKRQMA
SFYQPQKKRI RESEAEENQD SSGHFSNIPP LENPEDFDIV TETSFPIPGQ PCPSFPKSDV
YKATCDLATF QGDKMPPFQK YSSPRIYLPR PPCSYELANP GYTNSSPYPT LYKDSTSIPN
DTDWVHLNTL QCNVNSYSSY ERSFDFTNKQ HGWKPALGKP SLVERTNHGQ FQAMATRPYY
NPELPCRYLT TPPPGAPALQ TVITTTTKVS YQAYQPPAMK YSDSVREVKS LSSCNYAPED
TGMSVYPEPW GPPVTVTRAA SPSGPPPMKI AGDCRAIRPT VAIPHEPVSS RTDEAETWDV
CLSGLGSAVS YSDRVGPFFT YNNEDF*

speed

1.09 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