mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999780744898853 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr22:31491295G>CN/A show variant in all transcripts IGV

HGNC symbol

SMTN

Ensembl transcript ID

ENST00000347557

Genbank transcript ID

NM_006932

UniProt peptide

P53814

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1639G>C
cDNA.1857G>C
g.31205G>C

AA changes

A547P Score: 27 explain score(s)

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

547

frameshift

known variant

Reference ID: rs3205187

database	homozygous (C/C)	heterozygous	allele carriers
1000G	711	1040	1751
ExAC	21860	-10953	10907

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.122	0.837
	0.554	0.843
(flanking)	2.291	0.854

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	31196	wt: 0.9522 / mu: 0.9539 (marginal change - not scored)	wt: CATGCCCTCTCCCCACCCTGCAGATGGAAGCAGAGCCAGCA mu: CATGCCCTCTCCCCACCCTGCAGATGGAACCAGAGCCAGCA	ctgc\|AGAT
Acc marginally decreased	31198	wt: 0.9667 / mu: 0.9607 (marginal change - not scored)	wt: TGCCCTCTCCCCACCCTGCAGATGGAAGCAGAGCCAGCAGA mu: TGCCCTCTCCCCACCCTGCAGATGGAACCAGAGCCAGCAGA	gcag\|ATGG
Acc marginally increased	31195	wt: 0.2374 / mu: 0.2485 (marginal change - not scored)	wt: CCATGCCCTCTCCCCACCCTGCAGATGGAAGCAGAGCCAGC mu: CCATGCCCTCTCCCCACCCTGCAGATGGAACCAGAGCCAGC	cctg\|CAGA
Donor marginally increased	31197	wt: 0.2508 / mu: 0.2714 (marginal change - not scored)	wt: CCTGCAGATGGAAGC mu: CCTGCAGATGGAACC	TGCA\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

547

mutated

not conserved

547

Ptroglodytes

not conserved

ENSPTRG00000014259

397

Mmulatta

not conserved

ENSMMUG00000004675

547

Fcatus

not conserved

ENSFCAG00000001312

547

Mmusculus

not conserved

ENSMUSG00000020439

545

Ggallus

all identical

ENSGALG00000011865

539

EQPQAPRLQP

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074652

n/a

Dmelanogaster

no homologue

Celegans

no alignment

T15B12.1

n/a

Xtropicalis

all identical

ENSXETG00000016155

513

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2754 / 2754

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

918 / 918

position of stopcodon in wt / mu cDNA

2972 / 2972

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

219 / 219

chromosome

strand

last intron/exon boundary

2822

theoretical NMD boundary in CDS

2553

length of CDS

2754

coding sequence (CDS) position

1639

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

1857

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

31205

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

31491295

original gDNA sequence snippet

TCCCCACCCTGCAGATGGAAGCAGAGCCAGCAGAGCCTCTC

altered gDNA sequence snippet

TCCCCACCCTGCAGATGGAACCAGAGCCAGCAGAGCCTCTC

original cDNA sequence snippet

GCTGCAGCATCAAGATGGAAGCAGAGCCAGCAGAGCCTCTC

altered cDNA sequence snippet

GCTGCAGCATCAAGATGGAACCAGAGCCAGCAGAGCCTCTC

wildtype AA sequence

MADEALAGLD EGALRKLLEV TADLAERRRI RSAIRELQRQ ELEREEEALA SKRFRAERQD
NKENWLHSQQ REAEQRAALA RLAGQLESMN DVEELTALLR SAGEYEERKL IRAAIRRVRA
QEIEAATLAG RLYSGRPNSG SREDSKGLAA HRLEQCEVPE REEQEQQAEV SKPTPTPEGT
SQDVTTVTLL LRAPPGSTSS SPASPSSSPT PASPEPPLEP AEAQCLTAEV PGSPEPPPSP
PKTTSPEPQE SPTLPSTEGQ VVNKLLSGPK ETPAAQSPTR GPSDTKRADV AGPRPCQRSL
SVLSPRQPAQ NRESTPLASG PSSFQRAGSV RDRVHKFTSD SPMAARLQDG TPQAALSPLT
PARLLGPSLT STTPASSSSG SSSRGPSDTS SRFSKEQRGV AQPLAQLRSC PQEEGPRGRG
LAARPLENRA GGPVARSEEP GAPLPVAVGT AEPGGSMKTT FTIEIKDGRG QASTGRVLLP
TGNQRAELTL GLRAPPTLLS TSSGGKSTIT RVNSPGTLAR LGSVTHVTSF SHAPPSSRGG
CSIKMEAEPA EPLAAAVEAA NGAEQTRVNK APEGRSPLSA EELMTIEDEG VLDKMLDQST
DFEERKLIRA ALRELRQRKR DQRDKERERR LQEARGRPGE GRGNTATETT TRHSQRAADG
SAVSTVTKTE RLVHSNDGTR TARTTTVESS FVRRSENGSG STMMQTKTFS SSSSSKKMGS
IFDREDQASP RAGSLAALEK RQAEKKKELM KAQSLPKTSA SQARKAMIEK LEKEGAAGSP
GGPRAAVQRS TSFGVPNANS IKQMLLDWCR AKTRGYEHVD IQNFSSSWSD GMAFCALVHN
FFPEAFDYGQ LSPQNRRQNF EVAFSSAEML VDCVPLVEVD DMMIMGKKPD PKCVFTYVQS
LYNHLRRHEL RLRGKNV*

mutated AA sequence

MADEALAGLD EGALRKLLEV TADLAERRRI RSAIRELQRQ ELEREEEALA SKRFRAERQD
NKENWLHSQQ REAEQRAALA RLAGQLESMN DVEELTALLR SAGEYEERKL IRAAIRRVRA
QEIEAATLAG RLYSGRPNSG SREDSKGLAA HRLEQCEVPE REEQEQQAEV SKPTPTPEGT
SQDVTTVTLL LRAPPGSTSS SPASPSSSPT PASPEPPLEP AEAQCLTAEV PGSPEPPPSP
PKTTSPEPQE SPTLPSTEGQ VVNKLLSGPK ETPAAQSPTR GPSDTKRADV AGPRPCQRSL
SVLSPRQPAQ NRESTPLASG PSSFQRAGSV RDRVHKFTSD SPMAARLQDG TPQAALSPLT
PARLLGPSLT STTPASSSSG SSSRGPSDTS SRFSKEQRGV AQPLAQLRSC PQEEGPRGRG
LAARPLENRA GGPVARSEEP GAPLPVAVGT AEPGGSMKTT FTIEIKDGRG QASTGRVLLP
TGNQRAELTL GLRAPPTLLS TSSGGKSTIT RVNSPGTLAR LGSVTHVTSF SHAPPSSRGG
CSIKMEPEPA EPLAAAVEAA NGAEQTRVNK APEGRSPLSA EELMTIEDEG VLDKMLDQST
DFEERKLIRA ALRELRQRKR DQRDKERERR LQEARGRPGE GRGNTATETT TRHSQRAADG
SAVSTVTKTE RLVHSNDGTR TARTTTVESS FVRRSENGSG STMMQTKTFS SSSSSKKMGS
IFDREDQASP RAGSLAALEK RQAEKKKELM KAQSLPKTSA SQARKAMIEK LEKEGAAGSP
GGPRAAVQRS TSFGVPNANS IKQMLLDWCR AKTRGYEHVD IQNFSSSWSD GMAFCALVHN
FFPEAFDYGQ LSPQNRRQNF EVAFSSAEML VDCVPLVEVD DMMIMGKKPD PKCVFTYVQS
LYNHLRRHEL RLRGKNV*

speed

1.07 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