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: ENST00000430799
Querying Taster for transcript #2: ENST00000457599
Querying Taster for transcript #3: ENST00000324856
MT speed 0.61 s - this script 3.019986 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000457599	ARID1A	Deleterious	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000324856(MANE Select)	ARID1A	Deleterious	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000430799	ARID1A	Deleterious	148\|52	without_aae	No	Single base exchange	N/A

MutationT@ster 2025

Variant:

1:26697290A>C_2_ENST00000457599

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:26697290A>C (GRCh38)

Gene symbol

ARID1A

Gene constraints

LOEUF: 0.16, LOF (oe): 0.11, misssense (oe): 0.88, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000457599.7

Genbank transcript ID

NM_139135 (by similarity)

UniProt / AlphaMissense peptide

ARI1A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.887A>C
g.4055A>C

AA changes

AAE:	N296T	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		296	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T	S	P	S	S	A	R	G	Y
mutated	not conserved	296	G	T	P	Q	P	T	A	T	P	T	L	T	Q	L	L	T
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	820	REGION		lost
2	2285	CHAIN		lost
285	307	COMPBIAS	Polar residues	lost
295	299	MOTIF	LXXLL	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.683	1
	5.954	1
(flanking)	2.914	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

1

Strand

1

Original gDNA sequence snippet

CACCGCCACCCCCACCCTCAACCAACTGCTCACGTCGCCCA

Altered gDNA sequence snippet

CACCGCCACCCCCACCCTCACCCAACTGCTCACGTCGCCCA

Original cDNA sequence snippet

CACCGCCACCCCCACCCTCAACCAACTGCTCACGTCGCCCA

Altered cDNA sequence snippet

CACCGCCACCCCCACCCTCACCCAACTGCTCACGTCGCCCA

Wildtype AA sequence

MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG
PAVGPPQPLG KELQDGAESN GGGGGGGAGS GGGPGAEPDL KNSNGNAGPR PALNNNLTEP
PGGGGGGSSD GVGAPPHSAA AALPPPAYGF GQPYGRSPSA VAAAAAAVFH QQHGGQQSPG
LAALQSGGGG GLEPYAGPQQ NSHDHGFPNH QYNSYYPNRS AYPPPAPAYA LSSPRGGTPG
SGAAAAAGSK PPPSSSASAS SSSSSFAQQR FGAMGGGGPS AAGGGTPQPT ATPTLNQLLT
SPSSARGYQG YPGGDYSGGP QDGGAGKGPA DMASQCWGAA AAAAAAAAAS GGAQQRSHHA
PMSPGSSGGG GQPLARTPQP SSPMDQMGKM RPQPYGGTNP YSQQQGPPSG PQQGHGYPGQ
PYGSQTPQRY PMTMQGRAQS AMGGLSYTQQ IPPYGQQGPS GYGQQGQTPY YNQQSPHPQQ
QQPPYSQQPP SQTPHAQPSY QQQPQSQPPQ LQSSQPPYSQ QPSQPPHQQS PAPYPSQQST
TQQHPQSQPP YSQPQAQSPY QQQQPQQPAP STLSQQAAYP QPQSQQSQQT AYSQQRFPPP
QELSQDSFGS QASSAPSMTS SKGGQEDMNL SLQSRPSSLP DLSGSIDDLP MGTEGALSPG
VSTSGISSSQ GEQSNPAQSP FSPHTSPHLP GIRGPSPSPV GSPASVAQSR SGPLSPAAVP
GNQMPPRPPS GQSDSIMHPS MNQSSIAQDR GYMQRNPQMP QYSSPQPGSA LSPRQPSGGQ
IHTGMGSYQQ NSMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ
MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGGM NRKTQETAVA
MHVAANSIQN RPPGYPNMNQ GGMMGTGPPY GQGINSMAGM INPQGPPYSM GGTMANNSAG
MAASPEMMGL GDVKLTPATK MNNKADGTPK TESKSKKSSS STTTNEKITK LYELGGEPER
KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATNL
NVGTSSSAAS SLKKQYIQCL YAFECKIERG EDPPPDIFAA ADSKKSQPKI QPPSPAGSGS
MQGPQTPQST SSSMAEGGDL KPPTPASTPH SQIPPLPGMS RSNSVGIQDA FNDGSDSTFQ
KRNSMTPNPG YQPSMNTSDM MGRMSYEPNK DPYGSMRKAP GSDPFMSSGQ GPNGGMGDPY
SRAAGPGLGN VAMGPRQHYP YGGPYDRVRT EPGIGPEGNM STGAPQPNLM PSNPDSGMYS
PSRYPPQQQQ QQQQRHDSYG NQFSTQGTPS GSPFPSQQTT MYQQQQQVSS PAPLPRPMEN
RTSPSKSPFL HSGMKMQKAG PPVPASHIAP APVQPPMIRR DITFPPGSVE ATQPVLKQRR
RLTMKDIGTP EAWRVMMSLK SGLLAESTWA LDTINILLYD DNSIMTFNLS QLPGLLELLV
EYFRRCLIEI FGILKEYEVG DPGQRTLLDP GRFSKVSSPA PMEGGEEEEE LLGPKLEEEE
EEEVVENDEE IAFSGKDKPA SENSEEKLIS KFDKLPVKIV QKNDPFVVDC SDKLGRVQEF
DSGLLHWRIG GGDTTEHIQT HFESKTELLP SRPHAPCPPA PRKHVTTAEG TPGTTDQEGP
PPDGPPEKRI TATMDDMLST RSSTLTEDGA KSSEAIKESS KFPFGISPAQ SHRNIKILED
EPHSKDETPL CTLLDWQDSL AKRCVCVSNT IRSLSFVPGN DFEMSKHPGL LLILGKLILL
HHKHPERKQA PLTYEKEEEQ DQGVSCNKVE WWWDCLEMLR ENTLVTLANI SGQLDLSPYP
ESICLPVLDG LLHWAVCPSA EAQDPFSTLG PNAVLSPQRL VLETLSKLSI QDNNVDLILA
TPPFSRLEKL YSTMVRFLSD RKNPVCREMA VVLLANLAQG DSLAARAIAV QKGSIGNLLG
FLEDSLAATQ FQQSQASLLH MQNPPFEPTS VDMMRRAARA LLALAKVDEN HSEFTLYESR
LLDISVSPLM NSLVSQVICD VLFLIGQS*

Mutated AA sequence

MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG
PAVGPPQPLG KELQDGAESN GGGGGGGAGS GGGPGAEPDL KNSNGNAGPR PALNNNLTEP
PGGGGGGSSD GVGAPPHSAA AALPPPAYGF GQPYGRSPSA VAAAAAAVFH QQHGGQQSPG
LAALQSGGGG GLEPYAGPQQ NSHDHGFPNH QYNSYYPNRS AYPPPAPAYA LSSPRGGTPG
SGAAAAAGSK PPPSSSASAS SSSSSFAQQR FGAMGGGGPS AAGGGTPQPT ATPTLTQLLT
SPSSARGYQG YPGGDYSGGP QDGGAGKGPA DMASQCWGAA AAAAAAAAAS GGAQQRSHHA
PMSPGSSGGG GQPLARTPQP SSPMDQMGKM RPQPYGGTNP YSQQQGPPSG PQQGHGYPGQ
PYGSQTPQRY PMTMQGRAQS AMGGLSYTQQ IPPYGQQGPS GYGQQGQTPY YNQQSPHPQQ
QQPPYSQQPP SQTPHAQPSY QQQPQSQPPQ LQSSQPPYSQ QPSQPPHQQS PAPYPSQQST
TQQHPQSQPP YSQPQAQSPY QQQQPQQPAP STLSQQAAYP QPQSQQSQQT AYSQQRFPPP
QELSQDSFGS QASSAPSMTS SKGGQEDMNL SLQSRPSSLP DLSGSIDDLP MGTEGALSPG
VSTSGISSSQ GEQSNPAQSP FSPHTSPHLP GIRGPSPSPV GSPASVAQSR SGPLSPAAVP
GNQMPPRPPS GQSDSIMHPS MNQSSIAQDR GYMQRNPQMP QYSSPQPGSA LSPRQPSGGQ
IHTGMGSYQQ NSMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ
MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGGM NRKTQETAVA
MHVAANSIQN RPPGYPNMNQ GGMMGTGPPY GQGINSMAGM INPQGPPYSM GGTMANNSAG
MAASPEMMGL GDVKLTPATK MNNKADGTPK TESKSKKSSS STTTNEKITK LYELGGEPER
KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATNL
NVGTSSSAAS SLKKQYIQCL YAFECKIERG EDPPPDIFAA ADSKKSQPKI QPPSPAGSGS
MQGPQTPQST SSSMAEGGDL KPPTPASTPH SQIPPLPGMS RSNSVGIQDA FNDGSDSTFQ
KRNSMTPNPG YQPSMNTSDM MGRMSYEPNK DPYGSMRKAP GSDPFMSSGQ GPNGGMGDPY
SRAAGPGLGN VAMGPRQHYP YGGPYDRVRT EPGIGPEGNM STGAPQPNLM PSNPDSGMYS
PSRYPPQQQQ QQQQRHDSYG NQFSTQGTPS GSPFPSQQTT MYQQQQQVSS PAPLPRPMEN
RTSPSKSPFL HSGMKMQKAG PPVPASHIAP APVQPPMIRR DITFPPGSVE ATQPVLKQRR
RLTMKDIGTP EAWRVMMSLK SGLLAESTWA LDTINILLYD DNSIMTFNLS QLPGLLELLV
EYFRRCLIEI FGILKEYEVG DPGQRTLLDP GRFSKVSSPA PMEGGEEEEE LLGPKLEEEE
EEEVVENDEE IAFSGKDKPA SENSEEKLIS KFDKLPVKIV QKNDPFVVDC SDKLGRVQEF
DSGLLHWRIG GGDTTEHIQT HFESKTELLP SRPHAPCPPA PRKHVTTAEG TPGTTDQEGP
PPDGPPEKRI TATMDDMLST RSSTLTEDGA KSSEAIKESS KFPFGISPAQ SHRNIKILED
EPHSKDETPL CTLLDWQDSL AKRCVCVSNT IRSLSFVPGN DFEMSKHPGL LLILGKLILL
HHKHPERKQA PLTYEKEEEQ DQGVSCNKVE WWWDCLEMLR ENTLVTLANI SGQLDLSPYP
ESICLPVLDG LLHWAVCPSA EAQDPFSTLG PNAVLSPQRL VLETLSKLSI QDNNVDLILA
TPPFSRLEKL YSTMVRFLSD RKNPVCREMA VVLLANLAQG DSLAARAIAV QKGSIGNLLG
FLEDSLAATQ FQQSQASLLH MQNPPFEPTS VDMMRRAARA LLALAKVDEN HSEFTLYESR
LLDISVSPLM NSLVSQVICD VLFLIGQS*

Position of stopcodon in wt / mu CDS

6207 / 6207

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

2069 / 2069

Position of stopcodon in wt / mu cDNA

7447 / 7447

Position of start ATG in wt / mu cDNA

1241 / 1241

Last intron/exon boundary

5713

Theoretical NMD boundary in CDS

4422

Length of CDS

6207

Coding sequence (CDS) position

887

cDNA position

2127

gDNA position

4055

Chromosomal position

26697290

Speed

0.27 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:

1:26697290A>C_3_ENST00000324856

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:26697290A>C (GRCh38)

Gene symbol

ARID1A

Gene constraints

LOEUF: 0.14, LOF (oe): 0.10, misssense (oe): 0.88, synonymous (oe): 1.16 ? (gnomAD)

Ensembl transcript ID

ENST00000324856.13

Genbank transcript ID

NM_006015 (exact from MANE)

UniProt / AlphaMissense peptide

ARI1A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.887A>C
g.4055A>C

AA changes

AAE:	N296T	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		296	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T	S	P	S	S	A	R	G	Y
mutated	not conserved	296	G	T	P	Q	P	T	A	T	P	T	L	T	Q	L	L	T
Ptroglodytes	all identical	296	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T
Mmulatta	all identical	296	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T
Fcatus	all identical	296	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L
Mmusculus	all identical	297	G	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T	S	P	S	S	A	R	G
Ggallus	all identical	293	GGA	T	P	Q	P	T	A	T	P	T	L	N	Q	L	L	T	S	P	S	S	A	R	G
Trubripes	all identical	2536	G	T	Q	Q	P	T	S	T	P	T	L	N	Q
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no alignment	n/a

Protein features

Start (aa)	End (aa)	Feature	Details
1	820	REGION		lost
2	2285	CHAIN		lost
285	307	COMPBIAS	Polar residues	lost
295	299	MOTIF	LXXLL	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.683	1
	5.954	1
(flanking)	2.914	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

1

Strand

1

Original gDNA sequence snippet

CACCGCCACCCCCACCCTCAACCAACTGCTCACGTCGCCCA

Altered gDNA sequence snippet

CACCGCCACCCCCACCCTCACCCAACTGCTCACGTCGCCCA

Original cDNA sequence snippet

CACCGCCACCCCCACCCTCAACCAACTGCTCACGTCGCCCA

Altered cDNA sequence snippet

CACCGCCACCCCCACCCTCACCCAACTGCTCACGTCGCCCA

Wildtype AA sequence

MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG
PAVGPPQPLG KELQDGAESN GGGGGGGAGS GGGPGAEPDL KNSNGNAGPR PALNNNLTEP
PGGGGGGSSD GVGAPPHSAA AALPPPAYGF GQPYGRSPSA VAAAAAAVFH QQHGGQQSPG
LAALQSGGGG GLEPYAGPQQ NSHDHGFPNH QYNSYYPNRS AYPPPAPAYA LSSPRGGTPG
SGAAAAAGSK PPPSSSASAS SSSSSFAQQR FGAMGGGGPS AAGGGTPQPT ATPTLNQLLT
SPSSARGYQG YPGGDYSGGP QDGGAGKGPA DMASQCWGAA AAAAAAAAAS GGAQQRSHHA
PMSPGSSGGG GQPLARTPQP SSPMDQMGKM RPQPYGGTNP YSQQQGPPSG PQQGHGYPGQ
PYGSQTPQRY PMTMQGRAQS AMGGLSYTQQ IPPYGQQGPS GYGQQGQTPY YNQQSPHPQQ
QQPPYSQQPP SQTPHAQPSY QQQPQSQPPQ LQSSQPPYSQ QPSQPPHQQS PAPYPSQQST
TQQHPQSQPP YSQPQAQSPY QQQQPQQPAP STLSQQAAYP QPQSQQSQQT AYSQQRFPPP
QELSQDSFGS QASSAPSMTS SKGGQEDMNL SLQSRPSSLP DLSGSIDDLP MGTEGALSPG
VSTSGISSSQ GEQSNPAQSP FSPHTSPHLP GIRGPSPSPV GSPASVAQSR SGPLSPAAVP
GNQMPPRPPS GQSDSIMHPS MNQSSIAQDR GYMQRNPQMP QYSSPQPGSA LSPRQPSGGQ
IHTGMGSYQQ NSMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ
MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGGM NRKTQETAVA
MHVAANSIQN RPPGYPNMNQ GGMMGTGPPY GQGINSMAGM INPQGPPYSM GGTMANNSAG
MAASPEMMGL GDVKLTPATK MNNKADGTPK TESKSKKSSS STTTNEKITK LYELGGEPER
KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATNL
NVGTSSSAAS SLKKQYIQCL YAFECKIERG EDPPPDIFAA ADSKKSQPKI QPPSPAGSGS
MQGPQTPQST SSSMAEGGDL KPPTPASTPH SQIPPLPGMS RSNSVGIQDA FNDGSDSTFQ
KRNSMTPNPG YQPSMNTSDM MGRMSYEPNK DPYGSMRKAP GSDPFMSSGQ GPNGGMGDPY
SRAAGPGLGN VAMGPRQHYP YGGPYDRVRT EPGIGPEGNM STGAPQPNLM PSNPDSGMYS
PSRYPPQQQQ QQQQRHDSYG NQFSTQGTPS GSPFPSQQTT MYQQQQQNYK RPMDGTYGPP
AKRHEGEMYS VPYSTGQGQP QQQQLPPAQP QPASQQQAAQ PSPQQDVYNQ YGNAYPATAT
AATERRPAGG PQNQFPFQFG RDRVSAPPGT NAQQNMPPQM MGGPIQASAE VAQQGTMWQG
RNDMTYNYAN RQSTGSAPQG PAYHGVNRTD EMLHTDQRAN HEGSWPSHGT RQPPYGPSAP
VPPMTRPPPS NYQPPPSMQN HIPQVSSPAP LPRPMENRTS PSKSPFLHSG MKMQKAGPPV
PASHIAPAPV QPPMIRRDIT FPPGSVEATQ PVLKQRRRLT MKDIGTPEAW RVMMSLKSGL
LAESTWALDT INILLYDDNS IMTFNLSQLP GLLELLVEYF RRCLIEIFGI LKEYEVGDPG
QRTLLDPGRF SKVSSPAPME GGEEEEELLG PKLEEEEEEE VVENDEEIAF SGKDKPASEN
SEEKLISKFD KLPVKIVQKN DPFVVDCSDK LGRVQEFDSG LLHWRIGGGD TTEHIQTHFE
SKTELLPSRP HAPCPPAPRK HVTTAEGTPG TTDQEGPPPD GPPEKRITAT MDDMLSTRSS
TLTEDGAKSS EAIKESSKFP FGISPAQSHR NIKILEDEPH SKDETPLCTL LDWQDSLAKR
CVCVSNTIRS LSFVPGNDFE MSKHPGLLLI LGKLILLHHK HPERKQAPLT YEKEEEQDQG
VSCNKVEWWW DCLEMLRENT LVTLANISGQ LDLSPYPESI CLPVLDGLLH WAVCPSAEAQ
DPFSTLGPNA VLSPQRLVLE TLSKLSIQDN NVDLILATPP FSRLEKLYST MVRFLSDRKN
PVCREMAVVL LANLAQGDSL AARAIAVQKG SIGNLLGFLE DSLAATQFQQ SQASLLHMQN
PPFEPTSVDM MRRAARALLA LAKVDENHSE FTLYESRLLD ISVSPLMNSL VSQVICDVLF
LIGQS*

Mutated AA sequence

MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG
PAVGPPQPLG KELQDGAESN GGGGGGGAGS GGGPGAEPDL KNSNGNAGPR PALNNNLTEP
PGGGGGGSSD GVGAPPHSAA AALPPPAYGF GQPYGRSPSA VAAAAAAVFH QQHGGQQSPG
LAALQSGGGG GLEPYAGPQQ NSHDHGFPNH QYNSYYPNRS AYPPPAPAYA LSSPRGGTPG
SGAAAAAGSK PPPSSSASAS SSSSSFAQQR FGAMGGGGPS AAGGGTPQPT ATPTLTQLLT
SPSSARGYQG YPGGDYSGGP QDGGAGKGPA DMASQCWGAA AAAAAAAAAS GGAQQRSHHA
PMSPGSSGGG GQPLARTPQP SSPMDQMGKM RPQPYGGTNP YSQQQGPPSG PQQGHGYPGQ
PYGSQTPQRY PMTMQGRAQS AMGGLSYTQQ IPPYGQQGPS GYGQQGQTPY YNQQSPHPQQ
QQPPYSQQPP SQTPHAQPSY QQQPQSQPPQ LQSSQPPYSQ QPSQPPHQQS PAPYPSQQST
TQQHPQSQPP YSQPQAQSPY QQQQPQQPAP STLSQQAAYP QPQSQQSQQT AYSQQRFPPP
QELSQDSFGS QASSAPSMTS SKGGQEDMNL SLQSRPSSLP DLSGSIDDLP MGTEGALSPG
VSTSGISSSQ GEQSNPAQSP FSPHTSPHLP GIRGPSPSPV GSPASVAQSR SGPLSPAAVP
GNQMPPRPPS GQSDSIMHPS MNQSSIAQDR GYMQRNPQMP QYSSPQPGSA LSPRQPSGGQ
IHTGMGSYQQ NSMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ
MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGGM NRKTQETAVA
MHVAANSIQN RPPGYPNMNQ GGMMGTGPPY GQGINSMAGM INPQGPPYSM GGTMANNSAG
MAASPEMMGL GDVKLTPATK MNNKADGTPK TESKSKKSSS STTTNEKITK LYELGGEPER
KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATNL
NVGTSSSAAS SLKKQYIQCL YAFECKIERG EDPPPDIFAA ADSKKSQPKI QPPSPAGSGS
MQGPQTPQST SSSMAEGGDL KPPTPASTPH SQIPPLPGMS RSNSVGIQDA FNDGSDSTFQ
KRNSMTPNPG YQPSMNTSDM MGRMSYEPNK DPYGSMRKAP GSDPFMSSGQ GPNGGMGDPY
SRAAGPGLGN VAMGPRQHYP YGGPYDRVRT EPGIGPEGNM STGAPQPNLM PSNPDSGMYS
PSRYPPQQQQ QQQQRHDSYG NQFSTQGTPS GSPFPSQQTT MYQQQQQNYK RPMDGTYGPP
AKRHEGEMYS VPYSTGQGQP QQQQLPPAQP QPASQQQAAQ PSPQQDVYNQ YGNAYPATAT
AATERRPAGG PQNQFPFQFG RDRVSAPPGT NAQQNMPPQM MGGPIQASAE VAQQGTMWQG
RNDMTYNYAN RQSTGSAPQG PAYHGVNRTD EMLHTDQRAN HEGSWPSHGT RQPPYGPSAP
VPPMTRPPPS NYQPPPSMQN HIPQVSSPAP LPRPMENRTS PSKSPFLHSG MKMQKAGPPV
PASHIAPAPV QPPMIRRDIT FPPGSVEATQ PVLKQRRRLT MKDIGTPEAW RVMMSLKSGL
LAESTWALDT INILLYDDNS IMTFNLSQLP GLLELLVEYF RRCLIEIFGI LKEYEVGDPG
QRTLLDPGRF SKVSSPAPME GGEEEEELLG PKLEEEEEEE VVENDEEIAF SGKDKPASEN
SEEKLISKFD KLPVKIVQKN DPFVVDCSDK LGRVQEFDSG LLHWRIGGGD TTEHIQTHFE
SKTELLPSRP HAPCPPAPRK HVTTAEGTPG TTDQEGPPPD GPPEKRITAT MDDMLSTRSS
TLTEDGAKSS EAIKESSKFP FGISPAQSHR NIKILEDEPH SKDETPLCTL LDWQDSLAKR
CVCVSNTIRS LSFVPGNDFE MSKHPGLLLI LGKLILLHHK HPERKQAPLT YEKEEEQDQG
VSCNKVEWWW DCLEMLRENT LVTLANISGQ LDLSPYPESI CLPVLDGLLH WAVCPSAEAQ
DPFSTLGPNA VLSPQRLVLE TLSKLSIQDN NVDLILATPP FSRLEKLYST MVRFLSDRKN
PVCREMAVVL LANLAQGDSL AARAIAVQKG SIGNLLGFLE DSLAATQFQQ SQASLLHMQN
PPFEPTSVDM MRRAARALLA LAKVDENHSE FTLYESRLLD ISVSPLMNSL VSQVICDVLF
LIGQS*

Position of stopcodon in wt / mu CDS

6858 / 6858

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

2286 / 2286

Position of stopcodon in wt / mu cDNA

7247 / 7247

Position of start ATG in wt / mu cDNA

390 / 390

Last intron/exon boundary

5513

Theoretical NMD boundary in CDS

5073

Length of CDS

6858

Coding sequence (CDS) position

887

cDNA position

1276

gDNA position

4055

Chromosomal position

26697290

Speed

0.32 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:

1:26697290A>C_1_ENST00000430799

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Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 148|52 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:26697290A>C (GRCh38)

Gene symbol

ARID1A

Gene constraints

LOEUF: 0.10, LOF (oe): 0.06, misssense (oe): 0.72, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000430799.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.-13+3673A>C
g.4055A>C

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	5.683	1
	5.954	1
(flanking)	2.914	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

CACCGCCACCCCCACCCTCAACCAACTGCTCACGTCGCCCA

Altered gDNA sequence snippet

CACCGCCACCCCCACCCTCACCCAACTGCTCACGTCGCCCA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MDQMGKMRPQ PYGGTNPYSQ QQGPPSGPQQ GHGYPGQPYG SQTPQRYPMT MQGRAQSAMG
GLSYTQQIPP YGQQGPSGYG QQGQTPYYNQ QSPHPQQQQP PYSQQPPSQT PHAQPSYQQQ
PQSQPPQLQS SQPPYSQQPS QPPHQQSPAP YPSQQSTTQQ HPQSQPPYSQ PQAQSPYQQQ
QPQQPAPSTL SQQAAYPQPQ SQQSQQTAYS QQRFPPPQEL SQDSFGSQAS SAPSMTSSKG
GQEDMNLSLQ SRPSSLPDLS GSIDDLPMGT EGALSPGVST SGISSSQGEQ SNPAQSPFSP
HTSPHLPGIR GPSPSPVGSP ASVAQSRSGP LSPAAVPGNQ MPPRPPSGQS DSIMHPSMNQ
SSIAQDRGYM QRNPQMPQYS SPQPGSALSP RQPSGGQIHT GMGSYQQNSM GSYGPQGGQY
GPQGGYPRQP NYNALPNANY PSAGMAGGIN PMGAGGQMHG QPGIPPYGTL PPGRMSHASM
GNRPYGPNMA NMPPQVGSGM CPPPGGMNRK TQETAVAMHV AANSIQNRPP GYPNMNQGGM
MGTGPPYGQG INSMAGMINP QGPPYSMGGT MANNSAGMAA SPEMMGLGDV KLTPATKMNN
KADGTPKTES KSKKSSSSTT TNEKITKLYE LGGEPERKMW VDRYLAFTEE KAMGMTNLPA
VGRKPLDLYR LYVSVKEIGG LTQVNKNKKW RELATNLNVG TSSSAASSLK KQYIQCLYAF
ECKIERGEDP PPDIFAAADS KKSQPKIQPP SPAGSGSMQG PQTPQSTSSS MAEGGDLKPP
TPASTPHSQI PPLPGMRSNS VGIQDAFNDG SDSTFQKRNS MTPNPGYQPS MNTSDMMGRM
SYEPNKDPYG SMRKAPGSDP FMSSGQGPNG GMGDPYSRAA GPGLGNVAMG PRQHYPYGGP
YDRVRTEPGI GPEGNMSTGA PQPNLMPSNP DSGMYSPSRY PPQQQQQQQQ RHDSYGNQFS
TQGTPSGSPF PSQQTTMYQQ QQQNYKRPMD GTYGPPAKRH EGEMYSVPYS TGQGQPQQQQ
LPPAQPQPAS QQQAAQPSPQ QDVYNQYGNA YPATATAATE RRPAGGPQNQ FPFQFGRDRV
SAPPGTNAQQ NMPPQMMGGP IQASAEVAQQ GTMWQGRNDM TYNYANRQST GSAPQGPAYH
GVNRTDEMLH TDQRANHEGS WPSHGTRQPP YGPSAPVPPM TRPPPSNYQP PPSMQNHIPQ
VSSPAPLPRP MENRTSPSKS PFLHSGMKMQ KAGPPVPASH IAPAPVQPPM IRRDITFPPG
SVEATQPVLK QRRRLTMKDI GTPEAWRVMM SLKSGLLAES TWALDTINIL LYDDNSIMTF
NLSQLPGLLE LLVEYFRRCL IEIFGILKEY EVGDPGQRTL LDPGRFSKVS SPAPMEGGEE
EEELLGPKLE EEEEEEVVEN DEEIAFSGKD KPASENSEEK LISKFDKLPV KIVQKNDPFV
VDCSDKLGRV QEFDSGLLHW RIGGGDTTEH IQTHFESKTE LLPSRPHAPC PPAPRKHVTT
AEGTPGTTDQ EGPPPDGPPE KRITATMDDM LSTRSSTLTE DGAKSSEAIK ESSKFPFGIS
PAQSHRNIKI LEDEPHSKDE TPLCTLLDWQ DSLAKRCVCV SNTIRSLSFV PGNDFEMSKH
PGLLLILGKL ILLHHKHPER KQAPLTYEKE EEQDQGVSCN KVEWWWDCLE MLRENTLVTL
ANISGQLDLS PYPESICLPV LDGLLHWAVC PSAEAQDPFS TLGPNAVLSP QRLVLETLSK
LSIQDNNVDL ILATPPFSRL EKLYSTMVRF LSDRKNPVCR EMAVVLLANL AQGDSLAARA
IAVQKGSIGN LLGFLEDSLA ATQFQQSQAS LLHMQNPPFE PTSVDMMRRA ARALLALAKV
DENHSEFTLY ESRLLDISVS PLMNSLVSQV ICDVLFLIGQ S*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

395 / 395

Last intron/exon boundary

4366

Theoretical NMD boundary in CDS

3921

Length of CDS

5706

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

4055

Chromosomal position

26697290

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

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