MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000418611
Querying Taster for transcript #2: ENST00000389061
Querying Taster for transcript #3: ENST00000541314
MT speed 2.79 s - this script 3.970749 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SACM1L	polymorphism_automatic	0.999968421178393	simple_aae		affected		Y331F	single base exchange	rs1468542		show file
SACM1L	polymorphism_automatic	0.999968421178393	simple_aae		affected		Y434F	single base exchange	rs1468542		show file
SACM1L	polymorphism_automatic	0.999968421178393	simple_aae		affected		Y373F	single base exchange	rs1468542		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.15788216065901e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:45779136A>TN/A show variant in all transcripts IGV

HGNC symbol

SACM1L

Ensembl transcript ID

ENST00000418611

Genbank transcript ID

N/A

UniProt peptide

Q9NTJ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.992A>T
cDNA.1566A>T
g.48589A>T

AA changes

Y331F Score: 22 explain score(s)

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

331

frameshift

known variant

Reference ID: rs1468542

database	homozygous (T/T)	heterozygous	allele carriers
1000G	797	1152	1949
ExAC	22561	-12355	10206

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.921	1
	2.987	1
(flanking)	0.981	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
Donor increased	48591	wt: 0.27 / mu: 0.50	wt: TTTACAAAAATGGTA mu: TTTTCAAAAATGGTA	TACA\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

331

mutated

all conserved

331

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000002130

454

Fcatus

all identical

ENSFCAG00000006822

434

Mmusculus

all identical

ENSMUSG00000025240

434

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000003634

434

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0035195

433

Celegans

all conserved

F30A10.6

445

Xtropicalis

all identical

ENSXETG00000011975

230

protein features

start (aa)	end (aa)	feature	details
122	451	DOMAIN	SAC.	lost
376	376	CONFLICT	Q -> R (in Ref. 3; CAB66765).	might get lost (downstream of altered splice site)
456	456	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
521	541	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
549	569	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1455 / 1455

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

485 / 485

position of stopcodon in wt / mu cDNA

2029 / 2029

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

575 / 575

chromosome

strand

last intron/exon boundary

1893

theoretical NMD boundary in CDS

1268

length of CDS

1455

coding sequence (CDS) position

992

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

1566

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

48589

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

45779136

original gDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGGTAGGTCATTTC

altered gDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGGTAGGTCATTTC

original cDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGCCTGGGCTGACA

altered cDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGCCTGGGCTGACA

wildtype AA sequence

MLHLTDIQLQ DNKTFLAMLN HVLNVDGFYF STTYDLTHTL QRLSNTSPEF QEMSLLERAD
QRFVWNGHLL RELSAQPEVH RFALPVLHGF ITMHSCSING KYFDWILISR RSCFRAGVRY
YVRGIDSEGH AANFVETEQI VHYNGSKASF VQTRGSIPVF WSQRPNLKYK PLPQISKVAN
HMDGFQRHFD SQVIIYGKQV IINLINQKGS EKPLEQTFAT MVSSLGSGMM RYIAFDFHKE
CKNMRWDRLS ILLDQVAEMQ DELSYFLVDS AGQVVANQEG VFRSNCMDCL DRTNVIQSLL
ARRSLQAQLQ RLGVLHVGQK LEEQDEFEKI YKNAWADNAN ACAKQYAGTG ALKTDFTRTG
KRTHLGLIMD GWNSMIRYYK NNFSDGFRQD SIDLFLGNYS VDELESHSPL SVPRDWKFLA
LPIIMVVAFS MCIICLLMAG DTWTETLAYV LFWGVASIGT FFIILYNGKD FVDAPRLVQK
EKID*

mutated AA sequence

MLHLTDIQLQ DNKTFLAMLN HVLNVDGFYF STTYDLTHTL QRLSNTSPEF QEMSLLERAD
QRFVWNGHLL RELSAQPEVH RFALPVLHGF ITMHSCSING KYFDWILISR RSCFRAGVRY
YVRGIDSEGH AANFVETEQI VHYNGSKASF VQTRGSIPVF WSQRPNLKYK PLPQISKVAN
HMDGFQRHFD SQVIIYGKQV IINLINQKGS EKPLEQTFAT MVSSLGSGMM RYIAFDFHKE
CKNMRWDRLS ILLDQVAEMQ DELSYFLVDS AGQVVANQEG VFRSNCMDCL DRTNVIQSLL
ARRSLQAQLQ RLGVLHVGQK LEEQDEFEKI FKNAWADNAN ACAKQYAGTG ALKTDFTRTG
KRTHLGLIMD GWNSMIRYYK NNFSDGFRQD SIDLFLGNYS VDELESHSPL SVPRDWKFLA
LPIIMVVAFS MCIICLLMAG DTWTETLAYV LFWGVASIGT FFIILYNGKD FVDAPRLVQK
EKID*

speed

0.95 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
back to results table

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.15788216065901e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:45779136A>TN/A show variant in all transcripts IGV

HGNC symbol

SACM1L

Ensembl transcript ID

ENST00000389061

Genbank transcript ID

NM_014016

UniProt peptide

Q9NTJ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1301A>T
cDNA.1505A>T
g.48589A>T

AA changes

Y434F Score: 22 explain score(s)

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

434

frameshift

known variant

Reference ID: rs1468542

database	homozygous (T/T)	heterozygous	allele carriers
1000G	797	1152	1949
ExAC	22561	-12355	10206

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.921	1
	2.987	1
(flanking)	0.981	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
Donor increased	48591	wt: 0.27 / mu: 0.50	wt: TTTACAAAAATGGTA mu: TTTTCAAAAATGGTA	TACA\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

434

mutated

all conserved

434

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000002130

454

Fcatus

all identical

ENSFCAG00000006822

434

Mmusculus

all identical

ENSMUSG00000025240

434

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000003634

434

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0035195

433

Celegans

all conserved

F30A10.6

445

Xtropicalis

all identical

ENSXETG00000011975

230

protein features

start (aa)	end (aa)	feature	details
122	451	DOMAIN	SAC.	lost
456	456	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
521	541	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
549	569	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1764 / 1764

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

588 / 588

position of stopcodon in wt / mu cDNA

1968 / 1968

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

205 / 205

chromosome

strand

last intron/exon boundary

1832

theoretical NMD boundary in CDS

1577

length of CDS

1764

coding sequence (CDS) position

1301

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

1505

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

48589

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

45779136

original gDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGGTAGGTCATTTC

altered gDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGGTAGGTCATTTC

original cDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGCCTGGGCTGACA

altered cDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGCCTGGGCTGACA

wildtype AA sequence

MATAAYEQLK LHITPEKFYV EACDDGADDV LTIDRVSTEV TLAVKKDVPP SAVTRPIFGI
LGTIHLVAGN YLIVITKKIK VGEFFSHVVW KATDFDVLSY KKTMLHLTDI QLQDNKTFLA
MLNHVLNVDG FYFSTTYDLT HTLQRLSNTS PEFQEMSLLE RADQRFVWNG HLLRELSAQP
EVHRFALPVL HGFITMHSCS INGKYFDWIL ISRRSCFRAG VRYYVRGIDS EGHAANFVET
EQIVHYNGSK ASFVQTRGSI PVFWSQRPNL KYKPLPQISK VANHMDGFQR HFDSQVIIYG
KQVIINLINQ KGSEKPLEQT FATMVSSLGS GMMRYIAFDF HKECKNMRWD RLSILLDQVA
EMQDELSYFL VDSAGQVVAN QEGVFRSNCM DCLDRTNVIQ SLLARRSLQA QLQRLGVLHV
GQKLEEQDEF EKIYKNAWAD NANACAKQYA GTGALKTDFT RTGKRTHLGL IMDGWNSMIR
YYKNNFSDGF RQDSIDLFLG NYSVDELESH SPLSVPRDWK FLALPIIMVV AFSMCIICLL
MAGDTWTETL AYVLFWGVAS IGTFFIILYN GKDFVDAPRL VQKEKID*

mutated AA sequence

MATAAYEQLK LHITPEKFYV EACDDGADDV LTIDRVSTEV TLAVKKDVPP SAVTRPIFGI
LGTIHLVAGN YLIVITKKIK VGEFFSHVVW KATDFDVLSY KKTMLHLTDI QLQDNKTFLA
MLNHVLNVDG FYFSTTYDLT HTLQRLSNTS PEFQEMSLLE RADQRFVWNG HLLRELSAQP
EVHRFALPVL HGFITMHSCS INGKYFDWIL ISRRSCFRAG VRYYVRGIDS EGHAANFVET
EQIVHYNGSK ASFVQTRGSI PVFWSQRPNL KYKPLPQISK VANHMDGFQR HFDSQVIIYG
KQVIINLINQ KGSEKPLEQT FATMVSSLGS GMMRYIAFDF HKECKNMRWD RLSILLDQVA
EMQDELSYFL VDSAGQVVAN QEGVFRSNCM DCLDRTNVIQ SLLARRSLQA QLQRLGVLHV
GQKLEEQDEF EKIFKNAWAD NANACAKQYA GTGALKTDFT RTGKRTHLGL IMDGWNSMIR
YYKNNFSDGF RQDSIDLFLG NYSVDELESH SPLSVPRDWK FLALPIIMVV AFSMCIICLL
MAGDTWTETL AYVLFWGVAS IGTFFIILYN GKDFVDAPRL VQKEKID*

speed

0.91 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 3.15788216065901e-05 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:45779136A>TN/A show variant in all transcripts IGV

HGNC symbol

SACM1L

Ensembl transcript ID

ENST00000541314

Genbank transcript ID

N/A

UniProt peptide

Q9NTJ5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1118A>T
cDNA.1180A>T
g.48589A>T

AA changes

Y373F Score: 22 explain score(s)

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

373

frameshift

known variant

Reference ID: rs1468542

database	homozygous (T/T)	heterozygous	allele carriers
1000G	797	1152	1949
ExAC	22561	-12355	10206

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.921	1
	2.987	1
(flanking)	0.981	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
Donor increased	48591	wt: 0.27 / mu: 0.50	wt: TTTACAAAAATGGTA mu: TTTTCAAAAATGGTA	TACA\|aaaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

373

mutated

all conserved

373

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000002130

454

Fcatus

all identical

ENSFCAG00000006822

434

Mmusculus

all identical

ENSMUSG00000025240

434

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000003634

434

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0035195

433

Celegans

all conserved

F30A10.6

445

Xtropicalis

all identical

ENSXETG00000011975

230

protein features

start (aa)	end (aa)	feature	details
122	451	DOMAIN	SAC.	lost
376	376	CONFLICT	Q -> R (in Ref. 3; CAB66765).	might get lost (downstream of altered splice site)
456	456	MOD_RES	N6-acetyllysine.	might get lost (downstream of altered splice site)
521	541	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
549	569	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1581 / 1581

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

527 / 527

position of stopcodon in wt / mu cDNA

1643 / 1643

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

63 / 63

chromosome

strand

last intron/exon boundary

1507

theoretical NMD boundary in CDS

1394

length of CDS

1581

coding sequence (CDS) position

1118

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

1180

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

48589

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

45779136

original gDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGGTAGGTCATTTC

altered gDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGGTAGGTCATTTC

original cDNA sequence snippet

AGATGAATTTGAGAAGATTTACAAAAATGCCTGGGCTGACA

altered cDNA sequence snippet

AGATGAATTTGAGAAGATTTTCAAAAATGCCTGGGCTGACA

wildtype AA sequence

MWKLVMMEQM TYLPLTVCPQ RLPLQSRKMF LLQLSQDQYL VYWAQSIWWQ LQDNKTFLAM
LNHVLNVDGF YFSTTYDLTH TLQRLSNTSP EFQEMSLLER ADQRFVWNGH LLRELSAQPE
VHRFALPVLH GFITMHSCSI NGKYFDWILI SRRSCFRAGV RYYVRGIDSE GHAANFVETE
QIVHYNGSKA SFVQTRGSIP VFWSQRPNLK YKPLPQISKV ANHMDGFQRH FDSQVIIYGK
QVIINLINQK GSEKPLEQTF ATMVSSLGSG MMRYIAFDFH KECKNMRWDR LSILLDQVAE
MQDELSYFLV DSAGQVVANQ EGVFRSNCMD CLDRTNVIQS LLARRSLQAQ LQRLGVLHVG
QKLEEQDEFE KIYKNAWADN ANACAKQYAG TGALKTDFTR TGKRTHLGLI MDGWNSMIRY
YKNNFSDGFR QDSIDLFLGN YSVDELESHS PLSVPRDWKF LALPIIMVVA FSMCIICLLM
AGDTWTETLA YVLFWGVASI GTFFIILYNG KDFVDAPRLV QKEKID*

mutated AA sequence

MWKLVMMEQM TYLPLTVCPQ RLPLQSRKMF LLQLSQDQYL VYWAQSIWWQ LQDNKTFLAM
LNHVLNVDGF YFSTTYDLTH TLQRLSNTSP EFQEMSLLER ADQRFVWNGH LLRELSAQPE
VHRFALPVLH GFITMHSCSI NGKYFDWILI SRRSCFRAGV RYYVRGIDSE GHAANFVETE
QIVHYNGSKA SFVQTRGSIP VFWSQRPNLK YKPLPQISKV ANHMDGFQRH FDSQVIIYGK
QVIINLINQK GSEKPLEQTF ATMVSSLGSG MMRYIAFDFH KECKNMRWDR LSILLDQVAE
MQDELSYFLV DSAGQVVANQ EGVFRSNCMD CLDRTNVIQS LLARRSLQAQ LQRLGVLHVG
QKLEEQDEFE KIFKNAWADN ANACAKQYAG TGALKTDFTR TGKRTHLGLI MDGWNSMIRY
YKNNFSDGFR QDSIDLFLGN YSVDELESHS PLSVPRDWKF LALPIIMVVA FSMCIICLLM
AGDTWTETLA YVLFWGVASI GTFFIILYNG KDFVDAPRLV QKEKID*

speed

0.93 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems