MutationT@ster 2025

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...
Querying Taster for transcript #1: ENST00000296794
Querying Taster for transcript #2: ENST00000437974
Querying Taster for transcript #3: ENST00000426542
Querying Taster for transcript #4: ENST00000296799
Querying Taster for transcript #5: ENST00000545377
Querying Taster for transcript #6: ENST00000513042
MT speed 0.15 s - this script 2.542149 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000426542	ARHGEF28	Benign	135\|65	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000513042(MANE Select)	ARHGEF28	Benign	135\|65	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000296794	ARHGEF28	Benign	137\|63	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000296799	ARHGEF28	Benign	141\|59	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000437974	ARHGEF28	Benign	142\|58	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD
ENST00000545377	ARHGEF28	Benign	142\|58	without_aae	No	Single base exchange	Normal	Homozygous in gnomAD

MutationT@ster 2025

Variant:

5:73883847C>T_3_ENST00000426542

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 135|65 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.90, LOF (oe): 0.77, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000426542.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3018C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*

Mutated AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*

Position of stopcodon in wt / mu CDS

5118 / 5118

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

1706 / 1706

Position of stopcodon in wt / mu cDNA

5138 / 5138

Position of start ATG in wt / mu cDNA

21 / 21

Last intron/exon boundary

4968

Theoretical NMD boundary in CDS

4897

Length of CDS

5118

Coding sequence (CDS) position

3018

cDNA position

3038

gDNA position

257690

Chromosomal position

73883847

Speed

0.02 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:

5:73883847C>T_6_ENST00000513042

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 135|65 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.90, LOF (oe): 0.77, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000513042.7

Genbank transcript ID

NM_001177693 (exact from MANE), NM_001388076 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3018C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*

Mutated AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKND LDTSHTESPT PHDSNSHRPQ LQAFITEAKL
NLPTRTMTRQ DGETGDGAKE NIVYL*

Position of stopcodon in wt / mu CDS

5118 / 5118

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

1706 / 1706

Position of stopcodon in wt / mu cDNA

5256 / 5256

Position of start ATG in wt / mu cDNA

139 / 139

Last intron/exon boundary

5086

Theoretical NMD boundary in CDS

4897

Length of CDS

5118

Coding sequence (CDS) position

3018

cDNA position

3156

gDNA position

257690

Chromosomal position

73883847

Speed

0.03 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:

5:73883847C>T_1_ENST00000296794

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 137|63 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.90, LOF (oe): 0.78, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000296794.10

Genbank transcript ID

NM_001388078 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3018C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG N*

Mutated AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG N*

Position of stopcodon in wt / mu CDS

4956 / 4956

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

1652 / 1652

Position of stopcodon in wt / mu cDNA

5132 / 5132

Position of start ATG in wt / mu cDNA

177 / 177

Last intron/exon boundary

4823

Theoretical NMD boundary in CDS

4596

Length of CDS

4956

Coding sequence (CDS) position

3018

cDNA position

3194

gDNA position

257690

Chromosomal position

73883847

Speed

0.04 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:

5:73883847C>T_4_ENST00000296799

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 141|59 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.88, LOF (oe): 0.74, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000296799.8

Genbank transcript ID

NM_001244364 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2079C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MDSDSDSPFN YSWPSFPKMK IRRRTSKQDR SFDILKKSKP PSTLLAAGRL SDMLNGGDEV
YANCMVIDQV GDLDISYINI EGITATTSPE SRGCTLWPQS SKHTLPTETS PSVYPLSENV
EGTAHTEAQQ SFMSPSSSCA SNLNLSFGWH GFEKEQSHLK KRSSSLDALD ADSEGEGHSE
PSHICYTPGS QSSSRTGIPS GDELDSFETN TEPDFNISRA ESLPLSSNLQ SKESLLSGVR
SRSYSCSSPK ISLGKTRLVR ELTVCSSSEE QRAYSLSEPP RENRIQEEEW DKYIIPAKSE
SEKYKVSRTF SFLMNRMTSP RNKSKTKSKD AKDKEKLNRH QFAPGTFSGV LQCLVCDKTL
LGKESLQCSN CNANVHKGCK DAAPACTKKF QEKYNKNKPQ TILGNSSFRD IPQPGLSLHP
SSSVPVGLPT GRRETVGQVH PLSRSVPGTT LESFRRSATS LESESDHNSC RSRSHSDELL
QSMGSSPSTE SFIMEDVVDS SLWSDLSSDA QEFEAESWSL VVDPSFCNRQ EKDVIKRQDV
IFELMQTEMH HIQTLFIMSE IFRKGMKEEL QLDHSTVDKI FPCLDELLEI HRHFFYSMKE
RRQESCAGSD RNFVIDRIGD ILVQQFSEEN ASKMKKIYGE FCCHHKEAVN LFKELQQNKK
FQNFIKLRNS NLLARRRGIP ECILLVTQRI TKYPVLVERI LQYTKERTEE HKDLRKALCL
IKDMIATVDL KVNEYEKNQK WLEILNKIEN KTYTKLKNGH VFRKQALMSE ERTLLYDGLV
YWKTATGRFK DILALLLTDV LLFLQEKDQK YIFAAVDQKP SVISLQKLIA REVANEERGM
FLISASSAGP EMYEIHTNSK EERNNWMRRI QQAVESCPEE KGGRTSESDE DKRKAEARVA
KIQQCQEILT NQDQQICAYL EEKLHIYAEL GELSGFEDVH LEPHLLIKPD PGEPPQAASL
LAAALKEAES LQVAVKASQM GAVSQSCEDS CGDSVLADTL SSHDVPGSPT ASLVTGGREG
RGCSDVDPGI QGVVTDLAVS DAGEKVECRN FPGSSQSEII QAIQNLTRLL YSLQAALTIQ
DSHIEIHRLV LQQQEGLSLG HSILRGGPLQ DQKSRDADRQ HEELANVHQL QHQLQQEQRR
WLRRCEQQQR AQATRESWLQ ERERECQSQE ELLLRSRGEL DLQLQEYQHS LERLREGQRL
VEREQARMRA QQSLLGHWKH GRQRSLPAVL LPGGPEVMEL NRSESLCHEN SFFINEALVQ
MSFNTFNKLN PSVIHQDATY PTTQSHSDLV RTSEHQVDLK VDPSQPSNVS HKLWTAAGSG
HQILPFHESS KDSCKNDLDT SHTESPTPHD SNSHRPQLQA FITEAKLNLP TRTMTRQDGE
TGDGAKENIV YL*

Mutated AA sequence

MDSDSDSPFN YSWPSFPKMK IRRRTSKQDR SFDILKKSKP PSTLLAAGRL SDMLNGGDEV
YANCMVIDQV GDLDISYINI EGITATTSPE SRGCTLWPQS SKHTLPTETS PSVYPLSENV
EGTAHTEAQQ SFMSPSSSCA SNLNLSFGWH GFEKEQSHLK KRSSSLDALD ADSEGEGHSE
PSHICYTPGS QSSSRTGIPS GDELDSFETN TEPDFNISRA ESLPLSSNLQ SKESLLSGVR
SRSYSCSSPK ISLGKTRLVR ELTVCSSSEE QRAYSLSEPP RENRIQEEEW DKYIIPAKSE
SEKYKVSRTF SFLMNRMTSP RNKSKTKSKD AKDKEKLNRH QFAPGTFSGV LQCLVCDKTL
LGKESLQCSN CNANVHKGCK DAAPACTKKF QEKYNKNKPQ TILGNSSFRD IPQPGLSLHP
SSSVPVGLPT GRRETVGQVH PLSRSVPGTT LESFRRSATS LESESDHNSC RSRSHSDELL
QSMGSSPSTE SFIMEDVVDS SLWSDLSSDA QEFEAESWSL VVDPSFCNRQ EKDVIKRQDV
IFELMQTEMH HIQTLFIMSE IFRKGMKEEL QLDHSTVDKI FPCLDELLEI HRHFFYSMKE
RRQESCAGSD RNFVIDRIGD ILVQQFSEEN ASKMKKIYGE FCCHHKEAVN LFKELQQNKK
FQNFIKLRNS NLLARRRGIP ECILLVTQRI TKYPVLVERI LQYTKERTEE HKDLRKALCL
IKDMIATVDL KVNEYEKNQK WLEILNKIEN KTYTKLKNGH VFRKQALMSE ERTLLYDGLV
YWKTATGRFK DILALLLTDV LLFLQEKDQK YIFAAVDQKP SVISLQKLIA REVANEERGM
FLISASSAGP EMYEIHTNSK EERNNWMRRI QQAVESCPEE KGGRTSESDE DKRKAEARVA
KIQQCQEILT NQDQQICAYL EEKLHIYAEL GELSGFEDVH LEPHLLIKPD PGEPPQAASL
LAAALKEAES LQVAVKASQM GAVSQSCEDS CGDSVLADTL SSHDVPGSPT ASLVTGGREG
RGCSDVDPGI QGVVTDLAVS DAGEKVECRN FPGSSQSEII QAIQNLTRLL YSLQAALTIQ
DSHIEIHRLV LQQQEGLSLG HSILRGGPLQ DQKSRDADRQ HEELANVHQL QHQLQQEQRR
WLRRCEQQQR AQATRESWLQ ERERECQSQE ELLLRSRGEL DLQLQEYQHS LERLREGQRL
VEREQARMRA QQSLLGHWKH GRQRSLPAVL LPGGPEVMEL NRSESLCHEN SFFINEALVQ
MSFNTFNKLN PSVIHQDATY PTTQSHSDLV RTSEHQVDLK VDPSQPSNVS HKLWTAAGSG
HQILPFHESS KDSCKNDLDT SHTESPTPHD SNSHRPQLQA FITEAKLNLP TRTMTRQDGE
TGDGAKENIV YL*

Position of stopcodon in wt / mu CDS

4179 / 4179

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

1393 / 1393

Position of stopcodon in wt / mu cDNA

4250 / 4250

Position of start ATG in wt / mu cDNA

72 / 72

Last intron/exon boundary

4080

Theoretical NMD boundary in CDS

3958

Length of CDS

4179

Coding sequence (CDS) position

2079

cDNA position

2150

gDNA position

257690

Chromosomal position

73883847

Speed

0.02 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:

5:73883847C>T_2_ENST00000437974

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 142|58 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.89, LOF (oe): 0.77, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000437974.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3018C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*

Mutated AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*

Position of stopcodon in wt / mu CDS

5196 / 5196

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

1732 / 1732

Position of stopcodon in wt / mu cDNA

5216 / 5216

Position of start ATG in wt / mu cDNA

21 / 21

Last intron/exon boundary

5046

Theoretical NMD boundary in CDS

4975

Length of CDS

5196

Coding sequence (CDS) position

3018

cDNA position

3038

gDNA position

257690

Chromosomal position

73883847

Speed

0.02 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:

5:73883847C>T_5_ENST00000545377

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 142|58 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr5:73883847C>T (GRCh38)

Gene symbol

ARHGEF28

Gene constraints

LOEUF: 0.89, LOF (oe): 0.77, misssense (oe): 1.00, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000545377.5

Genbank transcript ID

NM_001080479 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3018C>T
g.257690C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs3749645
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	13827	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.889	1
	1.249	1
(flanking)	7.52	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

No

Chromosome

5

Strand

1

Original gDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered gDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Original cDNA sequence snippet

ACTCAGCGTATTACAAAATACCCTGTCTTGGTGGAAAGGAT

Altered cDNA sequence snippet

ACTCAGCGTATTACAAAATATCCTGTCTTGGTGGAAAGGAT

Wildtype AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*

Mutated AA sequence

MELSCSEAPL YGQMMIYAKF DKNVYLPEDA EFYFTYDGSH QRHVMIAERI EDNVLQSSVP
GHGLQETVTV SVCLCSEGYS PVTMGSGSVT YVDNMACRLA RLLVTQANRL TACSHQTLLT
PFALTAGALP ALDEELVLAL THLELPLEWT VLGSSSLEVS SHRESLLHLA MRWGLAKLSQ
FFLCLPGGVQ ALALPNEEGA TPLDLALREG HSKLVEDVTN FQGRWSPSFS RVQLSEEASL
HYIHSSETLT LTLNHTAEHL LEADIKLFRK YFWDRAFLVK AFEPEARPEE RTAMPSSGAE
TEEEIKNSVS SRSAAEKEDI KRVKSLVVQH NEHEDQHSLD LDRSFDILKK SKPPSTLLAA
GRLSDMLNGG DEVYANCMVI DQVGDLDISY INIEGITATT SPESRGCTLW PQSSKHTLPT
ETSPSVYPLS ENVEGTAHTE AQQSFMSPSS SCASNLNLSF GWHGFEKEQS HLKKRSSSLD
ALDADSEGEG HSEPSHICYT PGSQSSSRTG IPSGDELDSF ETNTEPDFNI SRAESLPLSS
NLQSKESLLS GVRSRSYSCS SPKISLGKTR LVRELTVCSS SEEQRAYSLS EPPRENRIQE
EEWDKYIIPA KSESEKYKVS RTFSFLMNRM TSPRNKSKTK SKDAKDKEKL NRHQFAPGTF
SGVLQCLVCD KTLLGKESLQ CSNCNANVHK GCKDAAPACT KKFQEKYNKN KPQTILGNSS
FRDIPQPGLS LHPSSSVPVG LPTGRRETVG QVHPLSRSVP GTTLESFRRS ATSLESESDH
NSCRSRSHSD ELLQSMGSSP STESFIMEDV VDSSLWSDLS SDAQEFEAES WSLVVDPSFC
NRQEKDVIKR QDVIFELMQT EMHHIQTLFI MSEIFRKGMK EELQLDHSTV DKIFPCLDEL
LEIHRHFFYS MKERRQESCA GSDRNFVIDR IGDILVQQFS EENASKMKKI YGEFCCHHKE
AVNLFKELQQ NKKFQNFIKL RNSNLLARRR GIPECILLVT QRITKYPVLV ERILQYTKER
TEEHKDLRKA LCLIKDMIAT VDLKVNEYEK NQKWLEILNK IENKTYTKLK NGHVFRKQAL
MSEERTLLYD GLVYWKTATG RFKDILALLL TDVLLFLQEK DQKYIFAAVD QKPSVISLQK
LIAREVANEE RGMFLISASS AGPEMYEIHT NSKEERNNWM RRIQQAVESC PEEKGGRTSE
SDEDKRKAEA RVAKIQQCQE ILTNQDQQIC AYLEEKLHIY AELGELSGFE DVHLEPHLLI
KPDPGEPPQA ASLLAAALKE AESLQVAVKA SQMGAVSQSC EDSCGDSVLA DTLSSHDVPG
SPTASLVTGG REGRGCSDVD PGIQGVVTDL AVSDAGEKVE CRNFPGSSQS EIIQAIQNLT
RLLYSLQAAL TIQDSHIEIH RLVLQQQEGL SLGHSILRGG PLQDQKSRDA DRQHEELANV
HQLQHQLQQE QRRWLRRCEQ QQRAQATRES WLQERERECQ SQEELLLRSR GELDLQLQEY
QHSLERLREG QRLVEREQAR MRAQQSLLGH WKHGRQRSLP AVLLPGGPEV MELNRSESLC
HENSFFINEA LVQMSFNTFN KLNPSVIHQD ATYPTTQSHS DLVRTSEHQV DLKVDPSQPS
NVSHKLWTAA GSGHQILPFH ESSKDSCKNG SSMTKCSCTL TSPPGLWTGT TSTLKDLDTS
HTESPTPHDS NSHRPQLQAF ITEAKLNLPT RTMTRQDGET GDGAKENIVY L*

Position of stopcodon in wt / mu CDS

5196 / 5196

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

1732 / 1732

Position of stopcodon in wt / mu cDNA

5372 / 5372

Position of start ATG in wt / mu cDNA

177 / 177

Last intron/exon boundary

5202

Theoretical NMD boundary in CDS

4975

Length of CDS

5196

Coding sequence (CDS) position

3018

cDNA position

3194

gDNA position

257690

Chromosomal position

73883847

Speed

0.02 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