MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000216373
Querying Taster for transcript #2: ENST00000543680
MT speed 0.74 s - this script 3.179265 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000216373(MANE Select)	SOS2	Deleterious	82\|18	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000543680	SOS2	Deleterious	93\|7	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

14:50145232C>T_1_ENST00000216373

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:50145232C>T (GRCh38)

Gene symbol

SOS2

Gene constraints

LOEUF: 0.41, LOF (oe): 0.28, misssense (oe): 0.85, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000216373.10

Genbank transcript ID

NM_006939 (exact from MANE)

UniProt / AlphaMissense peptide

SOS2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2605G>A
g.86347G>A

AA changes

AAE:	V869I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs373143128
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1	206	207

Protein conservation

Species	Match	AA	Alignment
Human		869	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S	V
mutated	all conserved	869	Q	V	F	Q	D	L	N	N	F	N	G	I	L	E	I	V	S	A	V	N	S	V	S
Ptroglodytes	all identical	869	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S
Mmulatta	all identical	869	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S
Fcatus	all identical	869	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S
Mmusculus	all identical	870	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S
Ggallus	all identical	868	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	M	N	S	V	S
Trubripes	all identical	872	Q	V	F	Q	E	L	N	N	F	N	G	V	L	E	V	V	S	A	I	N	S	V	P
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	870	Q	V	F	Q	E	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	P

Protein features

Start (aa)	End (aa)	Feature	Details
1	1332	CHAIN		lost
778	1017	DOMAIN	Ras-GEF	lost
866	876	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.26	1
	7.851	1
(flanking)	-0.374	0.119

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

14

Strand

-1

Original gDNA sequence snippet

ATTTGAATAATTTCAATGGCGTATTGGAGATAGTCAGTGCA

Altered gDNA sequence snippet

ATTTGAATAATTTCAATGGCATATTGGAGATAGTCAGTGCA

Original cDNA sequence snippet

ATTTGAATAATTTCAATGGCGTATTGGAGATAGTCAGTGCA

Altered cDNA sequence snippet

ATTTGAATAATTTCAATGGCATATTGGAGATAGTCAGTGCA

Wildtype AA sequence

MQQAPQPYEF FSEENSPKWR GLLVSALRKV QEQVHPTLSA NEESLYYIEE LIFQLLNKLC
MAQPRTVQDV EERVQKTFPH PIDKWAIADA QSAIEKRKRR NPLLLPVDKI HPSLKEVLGY
KVDYHVSLYI VAVLEYISAD ILKLAGNYVF NIRHYEISQQ DIKVSMCADK VLMDMFDQDD
IGLVSLCEDE PSSSGELNYY DLVRTEIAEE RQYLRELNMI IKVFREAFLS DRKLFKPSDI
EKIFSNISDI HELTVKLLGL IEDTVEMTDE SSPHPLAGSC FEDLAEEQAF DPYETLSQDI
LSPEFHEHFN KLMARPAVAL HFQSIADGFK EAVRYVLPRL MLVPVYHCWH YFELLKQLKA
CSEEQEDREC LNQAITALMN LQGSMDRIYK QYSPRRRPGD PVCPFYSHQL RSKHLAIKKM
NEIQKNIDGW EGKDIGQCCN EFIMEGPLTR IGAKHERHIF LFDGLMISCK PNHGQTRLPG
YSSAEYRLKE KFVMRKIQIC DKEDTCEHKH AFELVSKDEN SIIFAAKSAE EKNNWMAALI
SLHYRSTLDR MLDSVLLKEE NEQPLRLPSP EVYRFVVKDS EENIVFEDNL QSRSGIPIIK
GGTVVKLIER LTYHMYADPN FVRTFLTTYR SFCKPQELLS LLIERFEIPE PEPTDADKLA
IEKGEQPISA DLKRFRKEYV QPVQLRILNV FRHWVEHHFY DFERDLELLE RLESFISSVR
GKAMKKWVES IAKIIRRKKQ AQANGVSHNI TFESPPPPIE WHISKPGQFE TFDLMTLHPI
EIARQLTLLE SDLYRKVQPS ELVGSVWTKE DKEINSPNLL KMIRHTTNLT LWFEKCIVEA
ENFEERVAVL SRIIEILQVF QDLNNFNGVL EIVSAVNSVS VYRLDHTFEA LQERKRKILD
EAVELSQDHF KKYLVKLKSI NPPCVPFFGI YLTNILKTEE GNNDFLKKKG KDLINFSKRR
KVAEITGEIQ QYQNQPYCLR IEPDMRRFFE NLNPMGSASE KEFTDYLFNK SLEIEPRNCK
QPPRFPRKST FSLKSPGIRP NTGRHGSTSG TLRGHPTPLE REPCKISFSR IAETELESTV
SAPTSPNTPS TPPVSASSDL SVFLDVDLNS SCGSNSIFAP VLLPHSKSFF SSCGSLHKLS
EEPLIPPPLP PRKKFDHDAS NSKGNMKSDD DPPAIPPRQP PPPKVKPRVP VPTGAFDGPL
HSPPPPPPRD PLPDTPPPVP LRPPEHFINC PFNLQPPPLG HLHRDSDWLR DISTCPNSPS
TPPSTPSPRV PRRCYVLSSS QNNLAHPPAP PVPPRQNSSP HLPKLPPKTY KRELSHPPLY
RLPLLENAET PQ*

Mutated AA sequence

MQQAPQPYEF FSEENSPKWR GLLVSALRKV QEQVHPTLSA NEESLYYIEE LIFQLLNKLC
MAQPRTVQDV EERVQKTFPH PIDKWAIADA QSAIEKRKRR NPLLLPVDKI HPSLKEVLGY
KVDYHVSLYI VAVLEYISAD ILKLAGNYVF NIRHYEISQQ DIKVSMCADK VLMDMFDQDD
IGLVSLCEDE PSSSGELNYY DLVRTEIAEE RQYLRELNMI IKVFREAFLS DRKLFKPSDI
EKIFSNISDI HELTVKLLGL IEDTVEMTDE SSPHPLAGSC FEDLAEEQAF DPYETLSQDI
LSPEFHEHFN KLMARPAVAL HFQSIADGFK EAVRYVLPRL MLVPVYHCWH YFELLKQLKA
CSEEQEDREC LNQAITALMN LQGSMDRIYK QYSPRRRPGD PVCPFYSHQL RSKHLAIKKM
NEIQKNIDGW EGKDIGQCCN EFIMEGPLTR IGAKHERHIF LFDGLMISCK PNHGQTRLPG
YSSAEYRLKE KFVMRKIQIC DKEDTCEHKH AFELVSKDEN SIIFAAKSAE EKNNWMAALI
SLHYRSTLDR MLDSVLLKEE NEQPLRLPSP EVYRFVVKDS EENIVFEDNL QSRSGIPIIK
GGTVVKLIER LTYHMYADPN FVRTFLTTYR SFCKPQELLS LLIERFEIPE PEPTDADKLA
IEKGEQPISA DLKRFRKEYV QPVQLRILNV FRHWVEHHFY DFERDLELLE RLESFISSVR
GKAMKKWVES IAKIIRRKKQ AQANGVSHNI TFESPPPPIE WHISKPGQFE TFDLMTLHPI
EIARQLTLLE SDLYRKVQPS ELVGSVWTKE DKEINSPNLL KMIRHTTNLT LWFEKCIVEA
ENFEERVAVL SRIIEILQVF QDLNNFNGIL EIVSAVNSVS VYRLDHTFEA LQERKRKILD
EAVELSQDHF KKYLVKLKSI NPPCVPFFGI YLTNILKTEE GNNDFLKKKG KDLINFSKRR
KVAEITGEIQ QYQNQPYCLR IEPDMRRFFE NLNPMGSASE KEFTDYLFNK SLEIEPRNCK
QPPRFPRKST FSLKSPGIRP NTGRHGSTSG TLRGHPTPLE REPCKISFSR IAETELESTV
SAPTSPNTPS TPPVSASSDL SVFLDVDLNS SCGSNSIFAP VLLPHSKSFF SSCGSLHKLS
EEPLIPPPLP PRKKFDHDAS NSKGNMKSDD DPPAIPPRQP PPPKVKPRVP VPTGAFDGPL
HSPPPPPPRD PLPDTPPPVP LRPPEHFINC PFNLQPPPLG HLHRDSDWLR DISTCPNSPS
TPPSTPSPRV PRRCYVLSSS QNNLAHPPAP PVPPRQNSSP HLPKLPPKTY KRELSHPPLY
RLPLLENAET PQ*

Position of stopcodon in wt / mu CDS

3999 / 3999

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

1333 / 1333

Position of stopcodon in wt / mu cDNA

4294 / 4294

Position of start ATG in wt / mu cDNA

296 / 296

Last intron/exon boundary

3784

Theoretical NMD boundary in CDS

3438

Length of CDS

3999

Coding sequence (CDS) position

2605

cDNA position

2900

gDNA position

86347

Chromosomal position

50145232

Speed

0.33 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

14:50145232C>T_2_ENST00000543680

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 93|7 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr14:50145232C>T (GRCh38)

Gene symbol

SOS2

Gene constraints

LOEUF: 0.41, LOF (oe): 0.28, misssense (oe): 0.85, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000543680.5

Genbank transcript ID

NM_001411020 (by similarity)

UniProt / AlphaMissense peptide

SOS2_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2506G>A
g.86347G>A

AA changes

AAE:	V836I	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs373143128
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	1	206	207

Protein conservation

Species	Match	AA	Alignment
Human		836	Q	V	F	Q	D	L	N	N	F	N	G	V	L	E	I	V	S	A	V	N	S	V	S	V
mutated	all conserved	836	Q	V	F	Q	D	L	N	N	F	N	G	I	L	E	I	V
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	1332	CHAIN		lost
778	1017	DOMAIN	Ras-GEF	lost
817	838	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.26	1
	7.851	1
(flanking)	-0.374	0.119

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

14

Strand

-1

Original gDNA sequence snippet

ATTTGAATAATTTCAATGGCGTATTGGAGATAGTCAGTGCA

Altered gDNA sequence snippet

ATTTGAATAATTTCAATGGCATATTGGAGATAGTCAGTGCA

Original cDNA sequence snippet

ATTTGAATAATTTCAATGGCGTATTGGAGATAGTCAGTGCA

Altered cDNA sequence snippet

ATTTGAATAATTTCAATGGCATATTGGAGATAGTCAGTGCA

Wildtype AA sequence

MQQAPQPYEF FSEENSPKWR GLLVSALRKV QEQVHPTLSA NEESLYYIEE LIFQLLNKLC
MAQPRTVQDV EERVQKTFPH PIDKWAIADA QSAIEKRKRR NPLLLPVDKI HPSLKEVLGY
KVDYHVSLYI VAVLEYISAD ILKLAGNYVF NIRHYEISQQ DIKVSMCADK VLMDMFDQDD
IGLVSLCEDE PSSSGELNYY DLVRTEIAEE RQYLRELNMI IKVFREAFLS DRKLFKPSDI
EKIFSNISDI HELTVKLLGL IEDTVEMTDE SSPHPLAGSC FEDLAEEQAF DPYETLSQDI
LSPEFHEHFN KLMARPAVAL HFQQLKACSE EQEDRECLNQ AITALMNLQG SMDRIYKQYS
PRRRPGDPVC PFYSHQLRSK HLAIKKMNEI QKNIDGWEGK DIGQCCNEFI MEGPLTRIGA
KHERHIFLFD GLMISCKPNH GQTRLPGYSS AEYRLKEKFV MRKIQICDKE DTCEHKHAFE
LVSKDENSII FAAKSAEEKN NWMAALISLH YRSTLDRMLD SVLLKEENEQ PLRLPSPEVY
RFVVKDSEEN IVFEDNLQSR SGIPIIKGGT VVKLIERLTY HMYADPNFVR TFLTTYRSFC
KPQELLSLLI ERFEIPEPEP TDADKLAIEK GEQPISADLK RFRKEYVQPV QLRILNVFRH
WVEHHFYDFE RDLELLERLE SFISSVRGKA MKKWVESIAK IIRRKKQAQA NGVSHNITFE
SPPPPIEWHI SKPGQFETFD LMTLHPIEIA RQLTLLESDL YRKVQPSELV GSVWTKEDKE
INSPNLLKMI RHTTNLTLWF EKCIVEAENF EERVAVLSRI IEILQVFQDL NNFNGVLEIV
SAVNSVSVYR LDHTFEALQE RKRKILDEAV ELSQDHFKKY LVKLKSINPP CVPFFGIYLT
NILKTEEGNN DFLKKKGKDL INFSKRRKVA EITGEIQQYQ NQPYCLRIEP DMRRFFENLN
PMGSASEKEF TDYLFNKSLE IEPRNCKQPP RFPRKSTFSL KSPGIRPNTG RHGSTSGTLR
GHPTPLEREP CKISFSRIAE TELESTVSAP TSPNTPSTPP VSASSDLSVF LDVDLNSSCG
SNSIFAPVLL PHSKSFFSSC GSLHKLSEEP LIPPPLPPRK KFDHDASNSK GNMKSDDDPP
AIPPRQPPPP KVKPRVPVPT GAFDGPLHSP PPPPPRDPLP DTPPPVPLRP PEHFINCPFN
LQPPPLGHLH RDSDWLRDIS TCPNSPSTPP STPSPRVPRR CYVLSSSQNN LAHPPAPPVP
PRQNSSPHLP KLPPKTYKRE LSHPPLYRLP LLENAETPQ*

Mutated AA sequence

MQQAPQPYEF FSEENSPKWR GLLVSALRKV QEQVHPTLSA NEESLYYIEE LIFQLLNKLC
MAQPRTVQDV EERVQKTFPH PIDKWAIADA QSAIEKRKRR NPLLLPVDKI HPSLKEVLGY
KVDYHVSLYI VAVLEYISAD ILKLAGNYVF NIRHYEISQQ DIKVSMCADK VLMDMFDQDD
IGLVSLCEDE PSSSGELNYY DLVRTEIAEE RQYLRELNMI IKVFREAFLS DRKLFKPSDI
EKIFSNISDI HELTVKLLGL IEDTVEMTDE SSPHPLAGSC FEDLAEEQAF DPYETLSQDI
LSPEFHEHFN KLMARPAVAL HFQQLKACSE EQEDRECLNQ AITALMNLQG SMDRIYKQYS
PRRRPGDPVC PFYSHQLRSK HLAIKKMNEI QKNIDGWEGK DIGQCCNEFI MEGPLTRIGA
KHERHIFLFD GLMISCKPNH GQTRLPGYSS AEYRLKEKFV MRKIQICDKE DTCEHKHAFE
LVSKDENSII FAAKSAEEKN NWMAALISLH YRSTLDRMLD SVLLKEENEQ PLRLPSPEVY
RFVVKDSEEN IVFEDNLQSR SGIPIIKGGT VVKLIERLTY HMYADPNFVR TFLTTYRSFC
KPQELLSLLI ERFEIPEPEP TDADKLAIEK GEQPISADLK RFRKEYVQPV QLRILNVFRH
WVEHHFYDFE RDLELLERLE SFISSVRGKA MKKWVESIAK IIRRKKQAQA NGVSHNITFE
SPPPPIEWHI SKPGQFETFD LMTLHPIEIA RQLTLLESDL YRKVQPSELV GSVWTKEDKE
INSPNLLKMI RHTTNLTLWF EKCIVEAENF EERVAVLSRI IEILQVFQDL NNFNGILEIV
SAVNSVSVYR LDHTFEALQE RKRKILDEAV ELSQDHFKKY LVKLKSINPP CVPFFGIYLT
NILKTEEGNN DFLKKKGKDL INFSKRRKVA EITGEIQQYQ NQPYCLRIEP DMRRFFENLN
PMGSASEKEF TDYLFNKSLE IEPRNCKQPP RFPRKSTFSL KSPGIRPNTG RHGSTSGTLR
GHPTPLEREP CKISFSRIAE TELESTVSAP TSPNTPSTPP VSASSDLSVF LDVDLNSSCG
SNSIFAPVLL PHSKSFFSSC GSLHKLSEEP LIPPPLPPRK KFDHDASNSK GNMKSDDDPP
AIPPRQPPPP KVKPRVPVPT GAFDGPLHSP PPPPPRDPLP DTPPPVPLRP PEHFINCPFN
LQPPPLGHLH RDSDWLRDIS TCPNSPSTPP STPSPRVPRR CYVLSSSQNN LAHPPAPPVP
PRQNSSPHLP KLPPKTYKRE LSHPPLYRLP LLENAETPQ*

Position of stopcodon in wt / mu CDS

3900 / 3900

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

1300 / 1300

Position of stopcodon in wt / mu cDNA

3926 / 3926

Position of start ATG in wt / mu cDNA

27 / 27

Last intron/exon boundary

3416

Theoretical NMD boundary in CDS

3339

Length of CDS

3900

Coding sequence (CDS) position

2506

cDNA position

2532

gDNA position

86347

Chromosomal position

50145232

Speed

0.41 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table