MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 45|55 (del | benign) ?
Automatic classification due to ClinVar,
tree vote conflicts with the automatic classification ?
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000371139.9

Genbank transcript ID

NM_002351 (exact from MANE)

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
Ptroglodytes	all identical	7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
Mmulatta	all identical	7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
Fcatus	all identical	7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
Mmusculus	all identical	7	M	D	A	V	T	V	Y	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
Ggallus	all identical	7	M	E	A	L	P	I	Y	H	G	G	I	T	R	E	A	G	E	K	L	L	L	A
Trubripes	all identical	7	M	E	N	L	P	V	Y	H	G	P	I	G	K	E	E	G	E	R	R	L	G	Q
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	7	M	E	K	V	S	V	Y	H	G	N	I	S	R	E	M	G	E	K	L	L	S	D

Protein features

Start (aa)	End (aa)	Feature	Details
1	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

Position of stopcodon in wt / mu cDNA

467 / 467

Position of start ATG in wt / mu cDNA

81 / 81

Last intron/exon boundary

426

Theoretical NMD boundary in CDS

295

Length of CDS

387

Coding sequence (CDS) position

20

cDNA position

100

gDNA position

118795

Chromosomal position

124346662

Speed

0.28 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

MutationT@ster 2025

Variant:

23:124346662A>G_1_ENST00000698113

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000698113.1

Genbank transcript ID

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

Position of stopcodon in wt / mu cDNA

2075 / 2075

Position of start ATG in wt / mu cDNA

1689 / 1689

Last intron/exon boundary

2034

Theoretical NMD boundary in CDS

295

Length of CDS

387

Coding sequence (CDS) position

20

cDNA position

1708

gDNA position

118795

Chromosomal position

124346662

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

MutationT@ster 2025

Variant:

23:124346662A>G_2_ENST00000360027

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000360027.5

Genbank transcript ID

NM_001114937 (by similarity)

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGIREDPDV
CLKAP*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGIREDPDV
CLKAP*

Position of stopcodon in wt / mu CDS

378 / 378

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

126 / 126

Position of stopcodon in wt / mu cDNA

605 / 605

Position of start ATG in wt / mu cDNA

228 / 228

Last intron/exon boundary

564

Theoretical NMD boundary in CDS

286

Length of CDS

378

Coding sequence (CDS) position

20

cDNA position

247

gDNA position

118795

Chromosomal position

124346662

Speed

0.12 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

MutationT@ster 2025

Variant:

23:124346662A>G_3_ENST00000698116

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000698116.1

Genbank transcript ID

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

Position of stopcodon in wt / mu cDNA

516 / 516

Position of start ATG in wt / mu cDNA

130 / 130

Last intron/exon boundary

475

Theoretical NMD boundary in CDS

295

Length of CDS

387

Coding sequence (CDS) position

20

cDNA position

149

gDNA position

118795

Chromosomal position

124346662

Speed

0.11 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

MutationT@ster 2025

Variant:

23:124346662A>G_5_ENST00000477673

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000477673.2

Genbank transcript ID

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGI TVTFIHTECP RQKQVLGVLS
ISEARSRHCN TSAVSS*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGI TVTFIHTECP RQKQVLGVLS
ISEARSRHCN TSAVSS*

Position of stopcodon in wt / mu CDS

231 / 231

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

77 / 77

Position of stopcodon in wt / mu cDNA

285 / 285

Position of start ATG in wt / mu cDNA

55 / 55

Last intron/exon boundary

323

Theoretical NMD boundary in CDS

218

Length of CDS

231

Coding sequence (CDS) position

20

cDNA position

74

gDNA position

118795

Chromosomal position

124346662

Speed

0.26 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

MutationT@ster 2025

Variant:

23:124346662A>G_6_ENST00000494073

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000494073.5

Genbank transcript ID

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLISEA RSRHCNTSAV
SS*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLISEA RSRHCNTSAV
SS*

Position of stopcodon in wt / mu CDS

189 / 189

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

63 / 63

Position of stopcodon in wt / mu cDNA

243 / 243

Position of start ATG in wt / mu cDNA

55 / 55

Last intron/exon boundary

281

Theoretical NMD boundary in CDS

176

Length of CDS

189

Coding sequence (CDS) position

20

cDNA position

74

gDNA position

118795

Chromosomal position

124346662

Speed

0.23 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

MutationT@ster 2025

Variant:

23:124346662A>G_7_ENST00000698118

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 633415 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 54|46 (del | benign) ?
Automatic classification due to ClinVar
no values for phylogenetic conservation

Analysed issue

Analysis result

Variant

ChrX:124346662A>G (GRCh38)

Gene symbol

Gene constraints

no data

Ensembl transcript ID

ENST00000698118.1

Genbank transcript ID

UniProt / AlphaMissense peptide

SH21A_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.20A>G
g.118795A>G

AA changes

AAE:	Y7C	?
Score:	194

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

X-linked lymphoproliferative syndrome

pathogenic

Variant DBs

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

Protein conservation

Species	Match	AA
Human		7	M	D	A	V	A	V	Y	H	G	K	I	S	R	E	T	G	E	K	L
mutated	not conserved	7	M	D	A	V	A	V	C	H	G	K	I	S	R	E	T	G	E	K	L	L	L	A
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	128	CHAIN		lost
5	7	STRAND		lost
6	104	DOMAIN	SH2	lost

Phylogenetic conservation

	PhyloP	PhastCons

?

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

23

Strand

1

Original gDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered gDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Original cDNA sequence snippet

CATGGACGCAGTGGCTGTGTATCATGGCAAAATCAGCAGGG

Altered cDNA sequence snippet

CATGGACGCAGTGGCTGTGTGTCATGGCAAAATCAGCAGGG

Wildtype AA sequence

MDAVAVYHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Mutated AA sequence

MDAVAVCHGK ISRETGEKLL LATGLDGSYL LRDSESVPGV YCLCVLYHGY IYTYRVSQTE
TGSWSAETAP GVHKRYFRKI KNLISAFQKP DQGIVIPLQY PVEKKSSARS TQGTTGIRED
PDVCLKAP*

Position of stopcodon in wt / mu CDS

387 / 387

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

129 / 129

Position of stopcodon in wt / mu cDNA

422 / 422

Position of start ATG in wt / mu cDNA

36 / 36

Last intron/exon boundary

440

Theoretical NMD boundary in CDS

354

Length of CDS

387

Coding sequence (CDS) position

20

cDNA position

55

gDNA position

118795

Chromosomal position

124346662

Speed

0.11 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