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: ENST00000398958
Querying Taster for transcript #2: ENST00000649185
Querying Taster for transcript #3: ENST00000373833
Querying Taster for transcript #4: ENST00000373832
Querying Taster for transcript #5: ENST00000373831
Querying Taster for transcript #6: ENST00000683442
MT speed 0.39 s - this script 2.882729 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000649185	RCC1	Deleterious	98\|2	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000373831	RCC1	Deleterious	98\|2	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000683442(MANE Select)	RCC1	Deleterious	98\|2	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000398958	RCC1	Deleterious	100\|0	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000373833	RCC1	Deleterious	100\|0	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes
ENST00000373832	RCC1	Deleterious	100\|0	simple_aae	Yes	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected Splice site changes

MutationT@ster 2025

Variant:

1:28536747G>A_2_ENST00000649185

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.45, LOF (oe): 0.28, misssense (oe): 0.72, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000649185.1

Genbank transcript ID

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1031G>A
g.30805G>A

AA changes

AAE:	G344E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		344	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	344	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
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
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost
343	352	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKDTRAAA SRRVPGARSC QGACGPSPPD QKTRPVSHRS
HSTEPGLVLT LGQGDVGQLG LGENVMERKK PALVSIPEDV VQAEAGGMHT VCLSKSGQVY
SFGCNDEGAL GRDTSVEGSE MVPGKVELQE KVVQVSAGDS HTAALTDDGR VFLWGSFRDN
NGVIGLLEPM KKSMVPVQVQ LDVPVVKVAS GNDHLVMLTA DGDLYTLGCG EQGQLGRVPE
LFANRGGRQG LERLLVPKCV MLKSRGSRGH VRFQDAFCGA YFTFAISHEG HVYGFGLSNY
HQLGTPGTES CFIPQNLTSF KNSTKSWVGF SGGQHHTVCM DSEGKAYSLG RAEYGRLGLG
EGAEEKSIPT LISRLPAVSS VACGASVGYA VTKDGRVFAW GMGTNYQLGT GQDEDAWSPV
EMMGKQLENR VVLSVSSGGQ HTVLLVKDKE QS*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKDTRAAA SRRVPGARSC QGACGPSPPD QKTRPVSHRS
HSTEPGLVLT LGQGDVGQLG LGENVMERKK PALVSIPEDV VQAEAGGMHT VCLSKSGQVY
SFGCNDEGAL GRDTSVEGSE MVPGKVELQE KVVQVSAGDS HTAALTDDGR VFLWGSFRDN
NGVIGLLEPM KKSMVPVQVQ LDVPVVKVAS GNDHLVMLTA DGDLYTLGCG EQGQLGRVPE
LFANRGGRQG LERLLVPKCV MLKSRGSRGH VRFQDAFCGA YFTFAISHEG HVYGFGLSNY
HQLGTPGTES CFIPQNLTSF KNSTKSWVGF SGGQHHTVCM DSEEKAYSLG RAEYGRLGLG
EGAEEKSIPT LISRLPAVSS VACGASVGYA VTKDGRVFAW GMGTNYQLGT GQDEDAWSPV
EMMGKQLENR VVLSVSSGGQ HTVLLVKDKE QS*

Position of stopcodon in wt / mu CDS

1359 / 1359

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

453 / 453

Position of stopcodon in wt / mu cDNA

1725 / 1725

Position of start ATG in wt / mu cDNA

367 / 367

Last intron/exon boundary

1549

Theoretical NMD boundary in CDS

1132

Length of CDS

1359

Coding sequence (CDS) position

1031

cDNA position

1397

gDNA position

30805

Chromosomal position

28536747

Speed

0.07 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:

1:28536747G>A_5_ENST00000373831

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.45, LOF (oe): 0.28, misssense (oe): 0.72, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000373831.7

Genbank transcript ID

NM_001048194 (by similarity), NM_001048195 (by similarity)

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1031G>A
g.30805G>A

AA changes

AAE:	G344E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		344	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	344	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
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
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost
343	352	STRAND		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKDTRAAA SRRVPGARSC QGACGPSPPD QKTRPVSHRS
HSTEPGLVLT LGQGDVGQLG LGENVMERKK PALVSIPEDV VQAEAGGMHT VCLSKSGQVY
SFGCNDEGAL GRDTSVEGSE MVPGKVELQE KVVQVSAGDS HTAALTDDGR VFLWGSFRDN
NGVIGLLEPM KKSMVPVQVQ LDVPVVKVAS GNDHLVMLTA DGDLYTLGCG EQGQLGRVPE
LFANRGGRQG LERLLVPKCV MLKSRGSRGH VRFQDAFCGA YFTFAISHEG HVYGFGLSNY
HQLGTPGTES CFIPQNLTSF KNSTKSWVGF SGGQHHTVCM DSEGKAYSLG RAEYGRLGLG
EGAEEKSIPT LISRLPAVSS VACGASVGYA VTKDGRVFAW GMGTNYQLGT GQDEDAWSPV
EMMGKQLENR VVLSVSSGGQ HTVLLVKDKE QS*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKDTRAAA SRRVPGARSC QGACGPSPPD QKTRPVSHRS
HSTEPGLVLT LGQGDVGQLG LGENVMERKK PALVSIPEDV VQAEAGGMHT VCLSKSGQVY
SFGCNDEGAL GRDTSVEGSE MVPGKVELQE KVVQVSAGDS HTAALTDDGR VFLWGSFRDN
NGVIGLLEPM KKSMVPVQVQ LDVPVVKVAS GNDHLVMLTA DGDLYTLGCG EQGQLGRVPE
LFANRGGRQG LERLLVPKCV MLKSRGSRGH VRFQDAFCGA YFTFAISHEG HVYGFGLSNY
HQLGTPGTES CFIPQNLTSF KNSTKSWVGF SGGQHHTVCM DSEEKAYSLG RAEYGRLGLG
EGAEEKSIPT LISRLPAVSS VACGASVGYA VTKDGRVFAW GMGTNYQLGT GQDEDAWSPV
EMMGKQLENR VVLSVSSGGQ HTVLLVKDKE QS*

Position of stopcodon in wt / mu CDS

1359 / 1359

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

453 / 453

Position of stopcodon in wt / mu cDNA

1420 / 1420

Position of start ATG in wt / mu cDNA

62 / 62

Last intron/exon boundary

1244

Theoretical NMD boundary in CDS

1132

Length of CDS

1359

Coding sequence (CDS) position

1031

cDNA position

1092

gDNA position

30805

Chromosomal position

28536747

Speed

0.08 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:

1:28536747G>A_6_ENST00000683442

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 98|2 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.40, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000683442.1

Genbank transcript ID

NM_001381865 (exact from MANE), NM_001381866 (by similarity)

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.938G>A
g.30805G>A

AA changes

AAE:	G313E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		313	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	313	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
Ptroglodytes	all identical	344	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G
Mmulatta	all identical	330	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G
Fcatus	all identical	343	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G
Mmusculus	all identical	326	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G
Ggallus	all identical	309	G	Q	H	H	T	V	C	V	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G
Trubripes	all identical	322	G	Q	H	H	T	V	C	L	D	A	E	G	Q	V	Y	S	L	G	R	A	E	Y	G
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	329	G	Q	H	H	T	I	C	V	D	S	E	G	K	V	Y	S	L	G	R

Protein features

Start (aa)	End (aa)	Feature	Details
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEGKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEEKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Position of stopcodon in wt / mu CDS

1266 / 1266

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

422 / 422

Position of stopcodon in wt / mu cDNA

1569 / 1569

Position of start ATG in wt / mu cDNA

304 / 304

Last intron/exon boundary

1393

Theoretical NMD boundary in CDS

1039

Length of CDS

1266

Coding sequence (CDS) position

938

cDNA position

1241

gDNA position

30805

Chromosomal position

28536747

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:

1:28536747G>A_1_ENST00000398958

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.40, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000398958.6

Genbank transcript ID

NM_001048199 (by similarity)

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.938G>A
g.30805G>A

AA changes

AAE:	G313E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		313	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	313	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
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
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEGKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEEKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Position of stopcodon in wt / mu CDS

1266 / 1266

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

422 / 422

Position of stopcodon in wt / mu cDNA

1526 / 1526

Position of start ATG in wt / mu cDNA

261 / 261

Last intron/exon boundary

1350

Theoretical NMD boundary in CDS

1039

Length of CDS

1266

Coding sequence (CDS) position

938

cDNA position

1198

gDNA position

30805

Chromosomal position

28536747

Speed

0.08 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:

1:28536747G>A_3_ENST00000373833

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.40, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000373833.10

Genbank transcript ID

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.938G>A
g.30805G>A

AA changes

AAE:	G313E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		313	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	313	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
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
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEGKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEEKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Position of stopcodon in wt / mu CDS

1266 / 1266

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

422 / 422

Position of stopcodon in wt / mu cDNA

1551 / 1551

Position of start ATG in wt / mu cDNA

286 / 286

Last intron/exon boundary

1375

Theoretical NMD boundary in CDS

1039

Length of CDS

1266

Coding sequence (CDS) position

938

cDNA position

1223

gDNA position

30805

Chromosomal position

28536747

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:

1:28536747G>A_4_ENST00000373832

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected
Splice site changes

Model: simple_aae
Tree vote: 100|0 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:28536747G>A (GRCh38)

Gene symbol

RCC1

Gene constraints

LOEUF: 0.40, LOF (oe): 0.24, misssense (oe): 0.68, synonymous (oe): 0.94 ? (gnomAD)

Ensembl transcript ID

ENST00000373832.5

Genbank transcript ID

NM_001269 (by similarity)

UniProt / AlphaMissense peptide

RCC1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.938G>A
g.30805G>A

AA changes

AAE:	G313E	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1268238503
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA	Alignment
Human		313	G	Q	H	H	T	V	C	M	D	S	E	G	K	A	Y	S	L	G	R	A	E	Y	G	R
mutated	not conserved	313	G	Q	H	H	T	V	C	M	D	S	E	E	K	A	Y	S	L	G	R	A	E	Y	G
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
2	421	CHAIN		lost
312	362	REPEAT	RCC1	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	9.953	1
	9.953	1
(flanking)	0.258	0.986

?

Splice sites

MaxEntScan:

effect	gDNA position	score	sequence	exon-intron border
Acceptor weakened	30804	wt: 13.28 / mu: 11.72	-	wt: cctcccatag\|GAAAAGCATA mu: cctcccatag\|AAAAAGCATA

Distance from splice site

1

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGGAAAAGCATACAGCCTGGGCC

Altered gDNA sequence snippet

CTCTCTCCCTCCTCCCATAGAAAAAGCATACAGCCTGGGCC

Original cDNA sequence snippet

AGTCTGCATGGATTCGGAAGGAAAAGCATACAGCCTGGGCC

Altered cDNA sequence snippet

AGTCTGCATGGATTCGGAAGAAAAAGCATACAGCCTGGGCC

Wildtype AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEGKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Mutated AA sequence

MSPKRIAKRR SPPADAIPKS KKVKVSHRSH STEPGLVLTL GQGDVGQLGL GENVMERKKP
ALVSIPEDVV QAEAGGMHTV CLSKSGQVYS FGCNDEGALG RDTSVEGSEM VPGKVELQEK
VVQVSAGDSH TAALTDDGRV FLWGSFRDNN GVIGLLEPMK KSMVPVQVQL DVPVVKVASG
NDHLVMLTAD GDLYTLGCGE QGQLGRVPEL FANRGGRQGL ERLLVPKCVM LKSRGSRGHV
RFQDAFCGAY FTFAISHEGH VYGFGLSNYH QLGTPGTESC FIPQNLTSFK NSTKSWVGFS
GGQHHTVCMD SEEKAYSLGR AEYGRLGLGE GAEEKSIPTL ISRLPAVSSV ACGASVGYAV
TKDGRVFAWG MGTNYQLGTG QDEDAWSPVE MMGKQLENRV VLSVSSGGQH TVLLVKDKEQ
S*

Position of stopcodon in wt / mu CDS

1266 / 1266

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

422 / 422

Position of stopcodon in wt / mu cDNA

1448 / 1448

Position of start ATG in wt / mu cDNA

183 / 183

Last intron/exon boundary

1272

Theoretical NMD boundary in CDS

1039

Length of CDS

1266

Coding sequence (CDS) position

938

cDNA position

1120

gDNA position

30805

Chromosomal position

28536747

Speed

0.06 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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