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: ENST00000692089
Querying Taster for transcript #2: ENST00000402219
Querying Taster for transcript #3: ENST00000685279
Querying Taster for transcript #4: ENST00000395038
Querying Taster for transcript #5: ENST00000691229
MT speed 0.25 s - this script 2.64482 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000402219(MANE Select)	SOS1	Deleterious	88\|12	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000685279	SOS1	Deleterious	90\|10	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000691229	SOS1	Deleterious	93\|7	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000692089	SOS1	Deleterious	94\|6	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000395038	SOS1	Deleterious	94\|6	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

2:39022599A>G_2_ENST00000402219

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 88|12 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:39022599A>G (GRCh38)

Gene symbol

SOS1

Gene constraints

LOEUF: 0.29, LOF (oe): 0.18, misssense (oe): 0.79, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000402219.8

Genbank transcript ID

NM_005633 (exact from MANE), NM_001382394 (by similarity)

UniProt / AlphaMissense peptide

SOS1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1829T>C
g.101747T>C

AA changes

AAE:	I610T	?
Score:	89

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776146535
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	76	76

Protein conservation

Species	Match	AA	Alignment
Human		610	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P	N
mutated	not conserved	610			I	K	A	G	T	V	I	K	L	T	E	R	L	T	Y	H	M	Y	A	D	P
Ptroglodytes	all identical	610			I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P
Mmulatta	all identical	622	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P
Fcatus	all identical	610			I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P
Mmusculus	all identical	610			I	K	A	G	T	V	L	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P
Ggallus	all identical	624	P	I	I	K	A	G	T	V	V	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P
Trubripes	all identical	612	P	I	I	K	A	G	T	V	L	K	L	I	E	R	L	T	F	H	M	Y	A	D	P
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	616			I	K	A	G	T	V	V	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P

Protein features

Start (aa)	End (aa)	Feature	Details
1	1333	CHAIN		lost
597	741	DOMAIN	N-terminal Ras-GEF	lost
606	613	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.007	0.94
	9.197	1
(flanking)	7.908	1

?

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

2

Strand

-1

Original gDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered gDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Original cDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered cDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Wildtype AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAEEL AFDPYESYAR
DILRPGFHDR FLSQLSKPGA ALYLQSIGEG FKEAVQYVLP RLLLAPVYHC LHYFELLKQL
EEKSEDQEDK ECLKQAITAL LNVQSGMEKI CSKSLAKRRL SESACRFYSQ QMKGKQLAIK
KMNEIQKNID GWEGKDIGQC CNEFIMEGTL TRVGAKHERH IFLFDGLMIC CKSNHGQPRL
PGASNAEYRL KEKFFMRKVQ INDKDDTNEY KHAFEIILKD ENSVIFSAKS AEEKNNWMAA
LISLQYRSTL ERMLDVTMLQ EEKEEQMRLP SADVYRFAEP DSEENIIFEE NMQPKAGIPI
IKAGTVIKLI ERLTYHMYAD PNFVRTFLTT YRSFCKPQEL LSLIIERFEI PEPEPTEADR
IAIENGDQPL SAELKRFRKE YIQPVQLRVL NVCRHWVEHH FYDFERDAYL LQRMEEFIGT
VRGKAMKKWV ESITKIIQRK KIARDNGPGH NITFQSSPPT VEWHISRPGH IETFDLLTLH
PIEIARQLTL LESDLYRAVQ PSELVGSVWT KEDKEINSPN LLKMIRHTTN LTLWFEKCIV
ETENLEERVA VVSRIIEILQ VFQELNNFNG VLEVVSAMNS SPVYRLDHTF EQIPSRQKKI
LEEAHELSED HYKKYLAKLR SINPPCVPFF GIYLTNILKT EEGNPEVLKR HGKELINFSK
RRKVAEITGE IQQYQNQPYC LRVESDIKRF FENLNPMGNS MEKEFTDYLF NKSLEIEPRN
PKPLPRFPKK YSYPLKSPGV RPSNPRPGTM RHPTPLQQEP RKISYSRIPE SETESTASAP
NSPRTPLTPP PASGASSTTD VCSVFDSDHS SPFHSSNDTV FIQVTLPHGP RSASVSSISL
TKGTDEVPVP PPVPPRRRPE SAPAESSPSK IMSKHLDSPP AIPPRQPTSK AYSPRYSISD
RTSISDPPES PPLLPPREPV RTPDVFSSSP LHLQPPPLGK KSDHGNAFFP NSPSPFTPPP
PQTPSPHGTR RHLPSPPLTQ EVDLHSIAGP PVPPRQSTSQ HIPKLPPKTY KREHTHPSMH
RDGPPLLENA HSS*

Mutated AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAEEL AFDPYESYAR
DILRPGFHDR FLSQLSKPGA ALYLQSIGEG FKEAVQYVLP RLLLAPVYHC LHYFELLKQL
EEKSEDQEDK ECLKQAITAL LNVQSGMEKI CSKSLAKRRL SESACRFYSQ QMKGKQLAIK
KMNEIQKNID GWEGKDIGQC CNEFIMEGTL TRVGAKHERH IFLFDGLMIC CKSNHGQPRL
PGASNAEYRL KEKFFMRKVQ INDKDDTNEY KHAFEIILKD ENSVIFSAKS AEEKNNWMAA
LISLQYRSTL ERMLDVTMLQ EEKEEQMRLP SADVYRFAEP DSEENIIFEE NMQPKAGIPI
IKAGTVIKLT ERLTYHMYAD PNFVRTFLTT YRSFCKPQEL LSLIIERFEI PEPEPTEADR
IAIENGDQPL SAELKRFRKE YIQPVQLRVL NVCRHWVEHH FYDFERDAYL LQRMEEFIGT
VRGKAMKKWV ESITKIIQRK KIARDNGPGH NITFQSSPPT VEWHISRPGH IETFDLLTLH
PIEIARQLTL LESDLYRAVQ PSELVGSVWT KEDKEINSPN LLKMIRHTTN LTLWFEKCIV
ETENLEERVA VVSRIIEILQ VFQELNNFNG VLEVVSAMNS SPVYRLDHTF EQIPSRQKKI
LEEAHELSED HYKKYLAKLR SINPPCVPFF GIYLTNILKT EEGNPEVLKR HGKELINFSK
RRKVAEITGE IQQYQNQPYC LRVESDIKRF FENLNPMGNS MEKEFTDYLF NKSLEIEPRN
PKPLPRFPKK YSYPLKSPGV RPSNPRPGTM RHPTPLQQEP RKISYSRIPE SETESTASAP
NSPRTPLTPP PASGASSTTD VCSVFDSDHS SPFHSSNDTV FIQVTLPHGP RSASVSSISL
TKGTDEVPVP PPVPPRRRPE SAPAESSPSK IMSKHLDSPP AIPPRQPTSK AYSPRYSISD
RTSISDPPES PPLLPPREPV RTPDVFSSSP LHLQPPPLGK KSDHGNAFFP NSPSPFTPPP
PQTPSPHGTR RHLPSPPLTQ EVDLHSIAGP PVPPRQSTSQ HIPKLPPKTY KREHTHPSMH
RDGPPLLENA HSS*

Position of stopcodon in wt / mu CDS

4002 / 4002

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

1334 / 1334

Position of stopcodon in wt / mu cDNA

4631 / 4631

Position of start ATG in wt / mu cDNA

630 / 630

Last intron/exon boundary

4139

Theoretical NMD boundary in CDS

3459

Length of CDS

4002

Coding sequence (CDS) position

1829

cDNA position

2458

gDNA position

101747

Chromosomal position

39022599

Speed

0.05 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:

2:39022599A>G_3_ENST00000685279

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 90|10 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:39022599A>G (GRCh38)

Gene symbol

SOS1

Gene constraints

LOEUF: 0.35, LOF (oe): 0.21, misssense (oe): 0.79, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000685279.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.596T>C
g.101747T>C

AA changes

AAE:	I199T	?
Score:	89

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776146535
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	76	76

Protein conservation

Species	Match	AA	Alignment
Human		199	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P	N
mutated	not conserved	199	P	I	I	K	A	G	T	V	I	K	L	T	E	R	L	T	Y	H	M	Y	A	D	P
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.007	0.94
	9.197	1
(flanking)	7.908	1

?

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

2

Strand

-1

Original gDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered gDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Original cDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered cDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Wildtype AA sequence

MKGKQLAIKK MNEIQKNIDG WEGKDIGQCC NEFIMEGTLT RVGAKHERHI FLFDGLMICC
KSNHGQPRLP GASNAEYRLK EKFFMRKVQI NDKDDTNEYK HAFEIILKDE NSVIFSAKSA
EEKNNWMAAL ISLQYRSTLE RMLDVTMLQE EKEEQMRLPS ADVYRFAEPD SEENIIFEEN
MQPKAGIPII KAGTVIKLIE RLTYHMYADP NFVRTFLTTY RSFCKPQELL SLIIERFEIP
EPEPTEADRI AIENGDQPLS AELKRFRKEY IQPVQLRVLN VCRHWVEHHF YDFERDAYLL
QRMEEFIGTV RGKAMKKWVE SITKIIQRKK IARDNGPGHN ITFQSSPPTV EWHISRPGHI
ETFDLLTLHP IEIARQLTLL ESDLYRAVQP SELVGSVWTK EDKEINSPNL LKMIRHTTNL
TLWFEKCIVE TENLEERVAV VSRIIEILQV FQELNNFNGV LEVVSAMNSS PVYRLDHTFE
QIPSRQKKIL EEAHELSEDH YKKYLAKLRS INPPCVPFFG IYLTNILKTE EGNPEVLKRH
GKELINFSKR RKVAEITGEI QQYQNQPYCL RVESDIKRFF ENLNPMGNSM EKEFTDYLFN
KSLEIEPRNP KPLPRFPKKY SYPLKSPGVR PSNPRPGTMR HPTPLQQEPR KISYSRIPES
ETESTASAPN SPRTPLTPPP ASGASSTTDV CSVFDSDHSS PFHSSNDTVF IQVTLPHGPR
SASVSSISLT KGTDEVPVPP PVPPRRRPES APAESSPSKI MSKHLDSPPA IPPRQPTSKA
YSPRYSISDR TSISDPPESP PLLPPREPVR TPDVFSSSPL HLQPPPLGKK SDHGNAFFPN
SPSPFTPPPP QTPSPHGTRR HLPSPPLTQE VDLHSIAGPP VPPRQSTSQH IPKLPPKTYK
REHTHPSMHR DGPPLLENAH SS*

Mutated AA sequence

MKGKQLAIKK MNEIQKNIDG WEGKDIGQCC NEFIMEGTLT RVGAKHERHI FLFDGLMICC
KSNHGQPRLP GASNAEYRLK EKFFMRKVQI NDKDDTNEYK HAFEIILKDE NSVIFSAKSA
EEKNNWMAAL ISLQYRSTLE RMLDVTMLQE EKEEQMRLPS ADVYRFAEPD SEENIIFEEN
MQPKAGIPII KAGTVIKLTE RLTYHMYADP NFVRTFLTTY RSFCKPQELL SLIIERFEIP
EPEPTEADRI AIENGDQPLS AELKRFRKEY IQPVQLRVLN VCRHWVEHHF YDFERDAYLL
QRMEEFIGTV RGKAMKKWVE SITKIIQRKK IARDNGPGHN ITFQSSPPTV EWHISRPGHI
ETFDLLTLHP IEIARQLTLL ESDLYRAVQP SELVGSVWTK EDKEINSPNL LKMIRHTTNL
TLWFEKCIVE TENLEERVAV VSRIIEILQV FQELNNFNGV LEVVSAMNSS PVYRLDHTFE
QIPSRQKKIL EEAHELSEDH YKKYLAKLRS INPPCVPFFG IYLTNILKTE EGNPEVLKRH
GKELINFSKR RKVAEITGEI QQYQNQPYCL RVESDIKRFF ENLNPMGNSM EKEFTDYLFN
KSLEIEPRNP KPLPRFPKKY SYPLKSPGVR PSNPRPGTMR HPTPLQQEPR KISYSRIPES
ETESTASAPN SPRTPLTPPP ASGASSTTDV CSVFDSDHSS PFHSSNDTVF IQVTLPHGPR
SASVSSISLT KGTDEVPVPP PVPPRRRPES APAESSPSKI MSKHLDSPPA IPPRQPTSKA
YSPRYSISDR TSISDPPESP PLLPPREPVR TPDVFSSSPL HLQPPPLGKK SDHGNAFFPN
SPSPFTPPPP QTPSPHGTRR HLPSPPLTQE VDLHSIAGPP VPPRQSTSQH IPKLPPKTYK
REHTHPSMHR DGPPLLENAH SS*

Position of stopcodon in wt / mu CDS

2769 / 2769

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

923 / 923

Position of stopcodon in wt / mu cDNA

2836 / 2836

Position of start ATG in wt / mu cDNA

68 / 68

Last intron/exon boundary

2344

Theoretical NMD boundary in CDS

2226

Length of CDS

2769

Coding sequence (CDS) position

596

cDNA position

663

gDNA position

101747

Chromosomal position

39022599

Speed

0.05 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:

2:39022599A>G_5_ENST00000691229

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

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

Analysed issue

Analysis result

Variant

Chr2:39022599A>G (GRCh38)

Gene symbol

SOS1

Gene constraints

LOEUF: 0.15, LOF (oe): 0.06, misssense (oe): 0.78, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000691229.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1718T>C
g.101747T>C

AA changes

AAE:	I573T	?
Score:	89

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776146535
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	76	76

Protein conservation

Species	Match	AA	Alignment
Human		573	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P	N
mutated	not conserved	573	P	I	I	K	A	G	T	V	I	K	L	T	E	R	L	T	Y	H	M	Y	A	D	P
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.007	0.94
	9.197	1
(flanking)	7.908	1

?

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

2

Strand

-1

Original gDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered gDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Original cDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered cDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Wildtype AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAESI GEGFKEAVQY
VLPRLLLAPV YHCLHYFELL KQLEEKSEDQ EDKECLKQAI TALLNVQSGM EKICSKSLAK
RRLSESACRF YSQQMKGKQL AIKKMNEIQK NIDGWEGKDI GQCCNEFIME GTLTRVGAKH
ERHIFLFDGL MICCKSNHGQ PRLPGASNAE YRLKEKFFMR KVQINDKDDT NEYKHAFEII
LKDENSVIFS AKSAEEKNNW MAALISLQYR STLERMLDVT MLQEEKEEQM RLPSADVYRF
AEPDSEENII FEENMQPKAG IPIIKAGTVI KLIERLTYHM YADPNFVRTF LTTYRSFCKP
QELLSLIIER FEIPEPEPTE ADRIAIENGD QPLSAELKRF RKEYIQPVQL RVLNVCRHWV
EHHFYDFERD AYLLQRMEEF IGTVRGKAMK KWVESITKII QRKKIARDNG PGHNITFQSS
PPTVEWHISR PGHIETFDLL TLHPIEIARQ LTLLESDLYR CIVETENLEE RVAVVSRIIE
ILQVFQELNN FNGVLEVVSA MNSSPVYRLD HTFEQIPSRQ KKILEEAHEL SEDHYKKYLA
KLRSINPPCV PFFGIYLTNI LKTEEGNPEV LKRHGKELIN FSKRRKVAEI TGEIQQYQNQ
PYCLRVESDI KRFFENLNPM GNSMEKEFTD YLFNKSLEIE PRNPKPLPRF PKKYSYPLKS
PGVRPSNPRP GTMRHPTPLQ QEPRKISYSR IPESETESTA SAPNSPRTPL TPPPASGASS
TTDVCSVFDS DHSSPFHSSR CKNSKCIKVF VSTIHARGKK ESLLFFCMCE LVVKSNAISK
DNIIKI*

Mutated AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAESI GEGFKEAVQY
VLPRLLLAPV YHCLHYFELL KQLEEKSEDQ EDKECLKQAI TALLNVQSGM EKICSKSLAK
RRLSESACRF YSQQMKGKQL AIKKMNEIQK NIDGWEGKDI GQCCNEFIME GTLTRVGAKH
ERHIFLFDGL MICCKSNHGQ PRLPGASNAE YRLKEKFFMR KVQINDKDDT NEYKHAFEII
LKDENSVIFS AKSAEEKNNW MAALISLQYR STLERMLDVT MLQEEKEEQM RLPSADVYRF
AEPDSEENII FEENMQPKAG IPIIKAGTVI KLTERLTYHM YADPNFVRTF LTTYRSFCKP
QELLSLIIER FEIPEPEPTE ADRIAIENGD QPLSAELKRF RKEYIQPVQL RVLNVCRHWV
EHHFYDFERD AYLLQRMEEF IGTVRGKAMK KWVESITKII QRKKIARDNG PGHNITFQSS
PPTVEWHISR PGHIETFDLL TLHPIEIARQ LTLLESDLYR CIVETENLEE RVAVVSRIIE
ILQVFQELNN FNGVLEVVSA MNSSPVYRLD HTFEQIPSRQ KKILEEAHEL SEDHYKKYLA
KLRSINPPCV PFFGIYLTNI LKTEEGNPEV LKRHGKELIN FSKRRKVAEI TGEIQQYQNQ
PYCLRVESDI KRFFENLNPM GNSMEKEFTD YLFNKSLEIE PRNPKPLPRF PKKYSYPLKS
PGVRPSNPRP GTMRHPTPLQ QEPRKISYSR IPESETESTA SAPNSPRTPL TPPPASGASS
TTDVCSVFDS DHSSPFHSSR CKNSKCIKVF VSTIHARGKK ESLLFFCMCE LVVKSNAISK
DNIIKI*

Position of stopcodon in wt / mu CDS

3261 / 3261

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

1087 / 1087

Position of stopcodon in wt / mu cDNA

3278 / 3278

Position of start ATG in wt / mu cDNA

18 / 18

Last intron/exon boundary

2867

Theoretical NMD boundary in CDS

2799

Length of CDS

3261

Coding sequence (CDS) position

1718

cDNA position

1735

gDNA position

101747

Chromosomal position

39022599

Speed

0.05 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

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MutationT@ster 2025

Variant:

2:39022599A>G_1_ENST00000692089

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 94|6 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:39022599A>G (GRCh38)

Gene symbol

SOS1

Gene constraints

LOEUF: 0.14, LOF (oe): 0.06, misssense (oe): 0.78, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000692089.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1718T>C
g.101747T>C

AA changes

AAE:	I573T	?
Score:	89

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776146535
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	76	76

Protein conservation

Species	Match	AA	Alignment
Human		573	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P	N
mutated	not conserved	573	P	I	I	K	A	G	T	V	I	K	L	T	E	R	L	T	Y	H	M	Y	A	D	P
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.007	0.94
	9.197	1
(flanking)	7.908	1

?

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

2

Strand

-1

Original gDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered gDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Original cDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered cDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Wildtype AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAESI GEGFKEAVQY
VLPRLLLAPV YHCLHYFELL KQLEEKSEDQ EDKECLKQAI TALLNVQSGM EKICSKSLAK
RRLSESACRF YSQQMKGKQL AIKKMNEIQK NIDGWEGKDI GQCCNEFIME GTLTRVGAKH
ERHIFLFDGL MICCKSNHGQ PRLPGASNAE YRLKEKFFMR KVQINDKDDT NEYKHAFEII
LKDENSVIFS AKSAEEKNNW MAALISLQYR STLERMLDVT MLQEEKEEQM RLPSADVYRF
AEPDSEENII FEENMQPKAG IPIIKAGTVI KLIERLTYHM YADPNFVRTF LTTYRSFCKP
QELLSLIIER FEIPEPEPTE ADRIAIENGD QPLSAELKRF RKEYIQPVQL RVLNVCRHWV
EHHFYDFERD AYLLQRMEEF IGTVRGKAMK KWVESITKII QRKKIARDNG PGHNITFQSS
PPTVEWHISR PGHIETFDLL TLHPIEIARQ LTLLESDLYR AVQPSELVGS VWTKEDKEIN
SPNLLKMIRH TTNLTLWFEK CIVETENLEE RVAVVSRIIE ILQVFQELNN FNGVLEVVSA
MNSSPVYRLD HTFEQIPSRQ KKILEEAHEL SEDHYKKYLA KLRSINPPCV PFFGIYLTNI
LKTEEGNPEV LKRHGKELIN FSKRRKVAEI TGEIQQYQNQ PYCLRVESDI KRFFENLNPM
GNSMEKEFTD YLFNKSLEIE PRNPKPLPRF PKKYSYPLKS PGVRPSNPRP GTMRHPTPLQ
QEPRKISYSR IPESETESTA SAPNSPRTPL TPPPASGASS TTDVCSVFDS DHSSPFHSSN
DTVFIQVTLP HGPRSASVSS ISLTKGTDEV PVPPPVPPRR RPESAPAESS PSKRRGFTVL
TRMVLIS*

Mutated AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAESI GEGFKEAVQY
VLPRLLLAPV YHCLHYFELL KQLEEKSEDQ EDKECLKQAI TALLNVQSGM EKICSKSLAK
RRLSESACRF YSQQMKGKQL AIKKMNEIQK NIDGWEGKDI GQCCNEFIME GTLTRVGAKH
ERHIFLFDGL MICCKSNHGQ PRLPGASNAE YRLKEKFFMR KVQINDKDDT NEYKHAFEII
LKDENSVIFS AKSAEEKNNW MAALISLQYR STLERMLDVT MLQEEKEEQM RLPSADVYRF
AEPDSEENII FEENMQPKAG IPIIKAGTVI KLTERLTYHM YADPNFVRTF LTTYRSFCKP
QELLSLIIER FEIPEPEPTE ADRIAIENGD QPLSAELKRF RKEYIQPVQL RVLNVCRHWV
EHHFYDFERD AYLLQRMEEF IGTVRGKAMK KWVESITKII QRKKIARDNG PGHNITFQSS
PPTVEWHISR PGHIETFDLL TLHPIEIARQ LTLLESDLYR AVQPSELVGS VWTKEDKEIN
SPNLLKMIRH TTNLTLWFEK CIVETENLEE RVAVVSRIIE ILQVFQELNN FNGVLEVVSA
MNSSPVYRLD HTFEQIPSRQ KKILEEAHEL SEDHYKKYLA KLRSINPPCV PFFGIYLTNI
LKTEEGNPEV LKRHGKELIN FSKRRKVAEI TGEIQQYQNQ PYCLRVESDI KRFFENLNPM
GNSMEKEFTD YLFNKSLEIE PRNPKPLPRF PKKYSYPLKS PGVRPSNPRP GTMRHPTPLQ
QEPRKISYSR IPESETESTA SAPNSPRTPL TPPPASGASS TTDVCSVFDS DHSSPFHSSN
DTVFIQVTLP HGPRSASVSS ISLTKGTDEV PVPPPVPPRR RPESAPAESS PSKRRGFTVL
TRMVLIS*

Position of stopcodon in wt / mu CDS

3444 / 3444

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

1148 / 1148

Position of stopcodon in wt / mu cDNA

3461 / 3461

Position of start ATG in wt / mu cDNA

18 / 18

Last intron/exon boundary

3416

Theoretical NMD boundary in CDS

3348

Length of CDS

3444

Coding sequence (CDS) position

1718

cDNA position

1735

gDNA position

101747

Chromosomal position

39022599

Speed

0.05 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:

2:39022599A>G_4_ENST00000395038

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 94|6 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:39022599A>G (GRCh38)

Gene symbol

SOS1

Gene constraints

LOEUF: 0.29, LOF (oe): 0.18, misssense (oe): 0.79, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000395038.6

Genbank transcript ID

NM_001382395 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1829T>C
g.101747T>C

AA changes

AAE:	I610T	?
Score:	89

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs776146535
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	76	76

Protein conservation

Species	Match	AA	Alignment
Human		610	P	I	I	K	A	G	T	V	I	K	L	I	E	R	L	T	Y	H	M	Y	A	D	P	N
mutated	not conserved	610			I	K	A	G	T	V	I	K	L	T	E	R	L	T	Y	H	M	Y	A	D	P
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.007	0.94
	9.197	1
(flanking)	7.908	1

?

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

2

Strand

-1

Original gDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered gDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Original cDNA sequence snippet

AGGAACTGTTATTAAACTTATAGAGAGGCTTACGTACCATA

Altered cDNA sequence snippet

AGGAACTGTTATTAAACTTACAGAGAGGCTTACGTACCATA

Wildtype AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAEEL AFDPYESYAR
DILRPGFHDR FLSQLSKPGA ALYLQSIGEG FKEAVQYVLP RLLLAPVYHC LHYFELLKQL
EEKSEDQEDK ECLKQAITAL LNVQSGMEKI CSKSLAKRRL SESACRFYSQ QMKGKQLAIK
KMNEIQKNID GWEGKDIGQC CNEFIMEGTL TRVGAKHERH IFLFDGLMIC CKSNHGQPRL
PGASNAEYRL KEKFFMRKVQ INDKDDTNEY KHAFEIILKD ENSVIFSAKS AEEKNNWMAA
LISLQYRSTL ERMLDVTMLQ EEKEEQMRLP SADVYRFAEP DSEENIIFEE NMQPKAGIPI
IKAGTVIKLI ERLTYHMYAD PNFVRTFLTT YRSFCKPQEL LSLIIERFEI PEPEPTEADR
IAIENGDQPL SAELKRFRKE YIQPVQLRVL NVCRHWVEHH FYDFERDAYL LQRMEEFIGT
VRGKAMKKWV ESITKIIQRK KIARDNGPGH NITFQSSPPT VEWHISRPGH IETFDLLTLH
PIEIARQLTL LESDLYRAVQ PSELVGSVWT KEDKEINSPN LLKMIRHTTN LTLWFEKCIV
ETENLEERVA VVSRIIEILQ VFQELNNFNG VLEVVSAMNS SPVYRLDHTF EQIPSRQKKI
LEEAHELSED HYKKYLAKLR SINPPCVPFF GIYLTNILKT EEGNPEVLKR HGKELINFSK
RRKVAEITGE IQQYQNQPYC LRVESDIKRF FENLNPMGNS MEKEFTDYLF NKSLEIEPRN
PKPLPRFPKK YSYPLKSPGV RPSNPRPGTM RHPTPLQQEP RKISYSRIPE SETESTASAP
NSPRTPLTPP PASGASSTTD VCSVFDSDHS SPFHSRSASV SSISLTKGTD EVPVPPPVPP
RRRPESAPAE SSPSKIMSKH LDSPPAIPPR QPTSKAYSPR YSISDRTSIS DPPESPPLLP
PREPVRTPDV FSSSPLHLQP PPLGKKSDHG NAFFPNSPSP FTPPPPQTPS PHGTRRHLPS
PPLTQEVDLH SIAGPPVPPR QSTSQHIPKL PPKTYKREHT HPSMHRDGPP LLENAHSS*

Mutated AA sequence

MQAQQLPYEF FSEENAPKWR GLLVPALKKV QGQVHPTLES NDDALQYVEE LILQLLNMLC
QAQPRSASDV EERVQKSFPH PIDKWAIADA QSAIEKRKRR NPLSLPVEKI HPLLKEVLGY
KIDHQVSVYI VAVLEYISAD ILKLVGNYVR NIRHYEITKQ DIKVAMCADK VLMDMFHQDV
EDINILSLTD EEPSTSGEQT YYDLVKAFMA EIRQYIRELN LIIKVFREPF VSNSKLFSAN
DVENIFSRIV DIHELSVKLL GHIEDTVEMT DEGSPHPLVG SCFEDLAEEL AFDPYESYAR
DILRPGFHDR FLSQLSKPGA ALYLQSIGEG FKEAVQYVLP RLLLAPVYHC LHYFELLKQL
EEKSEDQEDK ECLKQAITAL LNVQSGMEKI CSKSLAKRRL SESACRFYSQ QMKGKQLAIK
KMNEIQKNID GWEGKDIGQC CNEFIMEGTL TRVGAKHERH IFLFDGLMIC CKSNHGQPRL
PGASNAEYRL KEKFFMRKVQ INDKDDTNEY KHAFEIILKD ENSVIFSAKS AEEKNNWMAA
LISLQYRSTL ERMLDVTMLQ EEKEEQMRLP SADVYRFAEP DSEENIIFEE NMQPKAGIPI
IKAGTVIKLT ERLTYHMYAD PNFVRTFLTT YRSFCKPQEL LSLIIERFEI PEPEPTEADR
IAIENGDQPL SAELKRFRKE YIQPVQLRVL NVCRHWVEHH FYDFERDAYL LQRMEEFIGT
VRGKAMKKWV ESITKIIQRK KIARDNGPGH NITFQSSPPT VEWHISRPGH IETFDLLTLH
PIEIARQLTL LESDLYRAVQ PSELVGSVWT KEDKEINSPN LLKMIRHTTN LTLWFEKCIV
ETENLEERVA VVSRIIEILQ VFQELNNFNG VLEVVSAMNS SPVYRLDHTF EQIPSRQKKI
LEEAHELSED HYKKYLAKLR SINPPCVPFF GIYLTNILKT EEGNPEVLKR HGKELINFSK
RRKVAEITGE IQQYQNQPYC LRVESDIKRF FENLNPMGNS MEKEFTDYLF NKSLEIEPRN
PKPLPRFPKK YSYPLKSPGV RPSNPRPGTM RHPTPLQQEP RKISYSRIPE SETESTASAP
NSPRTPLTPP PASGASSTTD VCSVFDSDHS SPFHSRSASV SSISLTKGTD EVPVPPPVPP
RRRPESAPAE SSPSKIMSKH LDSPPAIPPR QPTSKAYSPR YSISDRTSIS DPPESPPLLP
PREPVRTPDV FSSSPLHLQP PPLGKKSDHG NAFFPNSPSP FTPPPPQTPS PHGTRRHLPS
PPLTQEVDLH SIAGPPVPPR QSTSQHIPKL PPKTYKREHT HPSMHRDGPP LLENAHSS*

Position of stopcodon in wt / mu CDS

3957 / 3957

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

1319 / 1319

Position of stopcodon in wt / mu cDNA

3985 / 3985

Position of start ATG in wt / mu cDNA

29 / 29

Last intron/exon boundary

3493

Theoretical NMD boundary in CDS

3414

Length of CDS

3957

Coding sequence (CDS) position

1829

cDNA position

1857

gDNA position

101747

Chromosomal position

39022599

Speed

0.05 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