mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.0293939822523791 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM022820)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr14:64908845G>AN/A show variant in all transcripts IGV

HGNC symbol

MTHFD1

Ensembl transcript ID

ENST00000555709

Genbank transcript ID

NM_005956

UniProt peptide

P11586

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1958G>A
cDNA.2345G>A
g.54097G>A

AA changes

R653Q Score: 43 explain score(s)

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

653

frameshift

known variant

Reference ID: rs2236225

database	homozygous (A/A)	heterozygous	allele carriers
1000G	357	998	1355
ExAC	12202	8363	20565

known disease mutation at this position, please check HGMD for details (HGMD ID CM022820)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.088	1
	3.995	1
(flanking)	1.626	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 marginally increased	54097	wt: 0.2298 / mu: 0.2478 (marginal change - not scored)	wt: TTCCTCCATCATTGCAGACCGGATCGCACTCAAGCTTGTTG mu: TTCCTCCATCATTGCAGACCAGATCGCACTCAAGCTTGTTG	accg\|GATC
Acc marginally increased	54091	wt: 0.2176 / mu: 0.2475 (marginal change - not scored)	wt: TGGCAATTCCTCCATCATTGCAGACCGGATCGCACTCAAGC mu: TGGCAATTCCTCCATCATTGCAGACCAGATCGCACTCAAGC	ttgc\|AGAC
Donor increased	54092	wt: 0.54 / mu: 0.68	wt: ATTGCAGACCGGATC mu: ATTGCAGACCAGATC	TGCA\|gacc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

653

mutated

all conserved

653

Ptroglodytes

all identical

ENSPTRG00000006435

663

Mmulatta

all identical

ENSMMUG00000001319

652

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000021048

653

Ggallus

all conserved

ENSGALG00000011797

653

Trubripes

all conserved

ENSTRUG00000012569

655

Drerio

all conserved

ENSDARG00000040492

652

Dmelanogaster

not conserved

FBgn0020385

686

Celegans

all conserved

K07E3.4

356

Xtropicalis

all conserved

ENSXETG00000022511

279

protein features

start (aa)	end (aa)	feature	details
306	935	REGION	Formyltetrahydrofolate synthetase.	lost
786	786	MOD_RES	Phosphothreonine (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

2808 / 2808

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

936 / 936

position of stopcodon in wt / mu cDNA

3195 / 3195

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

388 / 388

chromosome

strand

last intron/exon boundary

3200

theoretical NMD boundary in CDS

2762

length of CDS

2808

coding sequence (CDS) position

1958

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

2345

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

54097

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

64908845

original gDNA sequence snippet

TTCCTCCATCATTGCAGACCGGATCGCACTCAAGCTTGTTG

altered gDNA sequence snippet

TTCCTCCATCATTGCAGACCAGATCGCACTCAAGCTTGTTG

original cDNA sequence snippet

TTCCTCCATCATTGCAGACCGGATCGCACTCAAGCTTGTTG

altered cDNA sequence snippet

TTCCTCCATCATTGCAGACCAGATCGCACTCAAGCTTGTTG

wildtype AA sequence

MAPAEILNGK EISAQIRARL KNQVTQLKEQ VPGFTPRLAI LQVGNRDDSN LYINVKLKAA
EEIGIKATHI KLPRTTTESE VMKYITSLNE DSTVHGFLVQ LPLDSENSIN TEEVINAIAP
EKDVDGLTSI NAGKLARGDL NDCFIPCTPK GCLELIKETG VPIAGRHAVV VGRSKIVGAP
MHDLLLWNNA TVTTCHSKTA HLDEEVNKGD ILVVATGQPE MVKGEWIKPG AIVIDCGINY
VPDDKKPNGR KVVGDVAYDE AKERASFITP VPGGVGPMTV AMLMQSTVES AKRFLEKFKP
GKWMIQYNNL NLKTPVPSDI DISRSCKPKP IGKLAREIGL LSEEVELYGE TKAKVLLSAL
ERLKHRPDGK YVVVTGITPT PLGEGKSTTT IGLVQALGAH LYQNVFACVR QPSQGPTFGI
KGGAAGGGYS QVIPMEEFNL HLTGDIHAIT AANNLVAAAI DARIFHELTQ TDKALFNRLV
PSVNGVRRFS DIQIRRLKRL GIEKTDPTTL TDEEINRFAR LDIDPETITW QRVLDTNDRF
LRKITIGQAP TEKGHTRTAQ FDISVASEIM AVLALTTSLE DMRERLGKMV VASSKKGEPV
SAEDLGVSGA LTVLMKDAIK PNLMQTLEGT PVFVHAGPFA NIAHGNSSII ADRIALKLVG
PEGFVVTEAG FGADIGMEKF FNIKCRYSGL CPHVVVLVAT VRALKMHGGG PTVTAGLPLP
KAYIQENLEL VEKGFSNLKK QIENARMFGI PVVVAVNAFK TDTESELDLI SRLSREHGAF
DAVKCTHWAE GGKGALALAQ AVQRAAQAPS SFQLLYDLKL PVEDKIRIIA QKIYGADDIE
LLPEAQHKAE VYTKQGFGNL PICMAKTHLS LSHNPEQKGV PTGFILPIRD IRASVGAGFL
YPLVGTMSTM PGLPTRPCFY DIDLDPETEQ VNGLF*

mutated AA sequence

MAPAEILNGK EISAQIRARL KNQVTQLKEQ VPGFTPRLAI LQVGNRDDSN LYINVKLKAA
EEIGIKATHI KLPRTTTESE VMKYITSLNE DSTVHGFLVQ LPLDSENSIN TEEVINAIAP
EKDVDGLTSI NAGKLARGDL NDCFIPCTPK GCLELIKETG VPIAGRHAVV VGRSKIVGAP
MHDLLLWNNA TVTTCHSKTA HLDEEVNKGD ILVVATGQPE MVKGEWIKPG AIVIDCGINY
VPDDKKPNGR KVVGDVAYDE AKERASFITP VPGGVGPMTV AMLMQSTVES AKRFLEKFKP
GKWMIQYNNL NLKTPVPSDI DISRSCKPKP IGKLAREIGL LSEEVELYGE TKAKVLLSAL
ERLKHRPDGK YVVVTGITPT PLGEGKSTTT IGLVQALGAH LYQNVFACVR QPSQGPTFGI
KGGAAGGGYS QVIPMEEFNL HLTGDIHAIT AANNLVAAAI DARIFHELTQ TDKALFNRLV
PSVNGVRRFS DIQIRRLKRL GIEKTDPTTL TDEEINRFAR LDIDPETITW QRVLDTNDRF
LRKITIGQAP TEKGHTRTAQ FDISVASEIM AVLALTTSLE DMRERLGKMV VASSKKGEPV
SAEDLGVSGA LTVLMKDAIK PNLMQTLEGT PVFVHAGPFA NIAHGNSSII ADQIALKLVG
PEGFVVTEAG FGADIGMEKF FNIKCRYSGL CPHVVVLVAT VRALKMHGGG PTVTAGLPLP
KAYIQENLEL VEKGFSNLKK QIENARMFGI PVVVAVNAFK TDTESELDLI SRLSREHGAF
DAVKCTHWAE GGKGALALAQ AVQRAAQAPS SFQLLYDLKL PVEDKIRIIA QKIYGADDIE
LLPEAQHKAE VYTKQGFGNL PICMAKTHLS LSHNPEQKGV PTGFILPIRD IRASVGAGFL
YPLVGTMSTM PGLPTRPCFY DIDLDPETEQ VNGLF*

speed

1.29 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