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: ENST00000620345
Querying Taster for transcript #2: ENST00000528354
Querying Taster for transcript #3: ENST00000397250
Querying Taster for transcript #4: ENST00000379971
Querying Taster for transcript #5: ENST00000397251
Querying Taster for transcript #6: ENST00000397248
Querying Taster for transcript #7: ENST00000525219
Querying Taster for transcript #8: ENST00000379977
MT speed 2.48 s - this script 6.778526 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000397250	IL15RA	Deleterious	51\|49	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000525219	IL15RA	Deleterious	52\|48	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000397248	IL15RA	Deleterious	54\|46	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000528354	IL15RA	Deleterious	56\|44	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000620345	IL15RA	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000397251	IL15RA	Benign	0\|200	without_aae	No	Single base exchange	N/A
ENST00000379971	IL15RA	Benign	1\|99	3utr	No	Single base exchange	N/A
ENST00000379977(MANE Select)	IL15RA	Benign	29\|71	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

10:5953195G>A_3_ENST00000397250

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 51|49 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.17, LOF (oe): 0.67, misssense (oe): 1.02, synonymous (oe): 1.17 ? (gnomAD)

Ensembl transcript ID

ENST00000397250.6

Genbank transcript ID

UniProt / AlphaMissense peptide

I15RA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.410C>T
g.24993C>T

AA changes

AAE:	P137L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

Species	Match	AA	Alignment
Human		137	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A	L
mutated	not conserved	137	L	A	C	Y	L	K	S	R	Q	T	P	L	L	A	S	V	E	M	E	A	M	E	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
31	205	TOPO_DOM	Extracellular	lost
31	267	CHAIN		lost
102	178	REGION		lost
105	178	COMPBIAS	Polar residues	lost
137	137	CARBOHYD	N-linked (GlcNAc...) asparagine	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRE PAASSPSSNN TAATTAAIVP GSQLMPSKSP
STGTTEISSH ESSHGTPSQT TAKNWELTAS ASHQPPGVYP QGHSDTTVAI STSTVLLCGL
SAVSLLACYL KSRQTPPLAS VEMEAMEALP VTWGTSSRDE DLENCSHHL*

Mutated AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRE PAASSPSSNN TAATTAAIVP GSQLMPSKSP
STGTTEISSH ESSHGTPSQT TAKNWELTAS ASHQPPGVYP QGHSDTTVAI STSTVLLCGL
SAVSLLACYL KSRQTPLLAS VEMEAMEALP VTWGTSSRDE DLENCSHHL*

Position of stopcodon in wt / mu CDS

510 / 510

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

170 / 170

Position of stopcodon in wt / mu cDNA

540 / 540

Position of start ATG in wt / mu cDNA

31 / 31

Last intron/exon boundary

428

Theoretical NMD boundary in CDS

347

Length of CDS

510

Coding sequence (CDS) position

410

cDNA position

440

gDNA position

24993

Chromosomal position

5953195

Speed

0.58 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:

10:5953195G>A_7_ENST00000525219

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 52|48 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.44, LOF (oe): 0.99, misssense (oe): 0.96, synonymous (oe): 1.06 ? (gnomAD)

Ensembl transcript ID

ENST00000525219.6

Genbank transcript ID

NM_001243539 (by similarity)

UniProt / AlphaMissense peptide

I15RA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.596C>T
g.24993C>T

AA changes

AAE:	P199L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

Species	Match	AA	Alignment
Human		199	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A	L
mutated	not conserved	199	L	A	C	Y	L	K	S	R	Q	T	P	L	L	A	S	V	E	M	E	A	M	E	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
31	205	TOPO_DOM	Extracellular	lost
31	267	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MSVEHADIWV KSYSLYSRER YICNSGFKRK AGTSSLTECV LNKATNVAHW TTPSLKCIRD
PALVHQRPAP PSTVTTAGVT PQPESLSPSG KEPAASSPSS NNTAATTAAI VPGSQLMPSK
SPSTGTTEIS SHESSHGTPS QTTAKNWELT ASASHQPPGV YPQGHSDTTV AISTSTVLLC
GLSAVSLLAC YLKSRQTPPL ASVEMEAMEA LPVTWGTSSR DEDLENCSHH L*

Mutated AA sequence

MSVEHADIWV KSYSLYSRER YICNSGFKRK AGTSSLTECV LNKATNVAHW TTPSLKCIRD
PALVHQRPAP PSTVTTAGVT PQPESLSPSG KEPAASSPSS NNTAATTAAI VPGSQLMPSK
SPSTGTTEIS SHESSHGTPS QTTAKNWELT ASASHQPPGV YPQGHSDTTV AISTSTVLLC
GLSAVSLLAC YLKSRQTPLL ASVEMEAMEA LPVTWGTSSR DEDLENCSHH L*

Position of stopcodon in wt / mu CDS

696 / 696

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

232 / 232

Position of stopcodon in wt / mu cDNA

1127 / 1127

Position of start ATG in wt / mu cDNA

432 / 432

Last intron/exon boundary

1015

Theoretical NMD boundary in CDS

533

Length of CDS

696

Coding sequence (CDS) position

596

cDNA position

1027

gDNA position

24993

Chromosomal position

5953195

Speed

0.37 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:

10:5953195G>A_6_ENST00000397248

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 54|46 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.50, LOF (oe): 1.05, misssense (oe): 1.12, synonymous (oe): 1.21 ? (gnomAD)

Ensembl transcript ID

ENST00000397248.6

Genbank transcript ID

NM_001256765 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.962C>T
g.24993C>T

AA changes

AAE:	P321L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

Species	Match	AA	Alignment
Human		321	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A	L
mutated	not conserved	321	L	A	C	Y	L	K	S	R	Q	T	P	L	L	A	S	V	E	M	E	A	M	E	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MRLAGRQVPE QRSPPPPGLG SARPGSPAVS CGAAAMAPRR ARGCRTLGLP ALLLLLLLRP
PATRDARDRL AVLAGRSRIS ESFNHEVQTH EACVRLRTME NCPQCHHHRT SRQQAGITCP
PPMSVEHADI WVKSYSLYSR ERYICNSGFK RKAGTSSLTE CVLNKATNVA HWTTPSLKCI
RDPALVHQRP APPSTVTTAG VTPQPESLSP SGKEPAASSP SSNNTAATTA AIVPGSQLMP
SKSPSTGTTE ISSHESSHGT PSQTTAKNWE LTASASHQPP GVYPQGHSDT TVAISTSTVL
LCGLSAVSLL ACYLKSRQTP PLASVEMEAM EALPVTWGTS SRDEDLENCS HHL*

Mutated AA sequence

MRLAGRQVPE QRSPPPPGLG SARPGSPAVS CGAAAMAPRR ARGCRTLGLP ALLLLLLLRP
PATRDARDRL AVLAGRSRIS ESFNHEVQTH EACVRLRTME NCPQCHHHRT SRQQAGITCP
PPMSVEHADI WVKSYSLYSR ERYICNSGFK RKAGTSSLTE CVLNKATNVA HWTTPSLKCI
RDPALVHQRP APPSTVTTAG VTPQPESLSP SGKEPAASSP SSNNTAATTA AIVPGSQLMP
SKSPSTGTTE ISSHESSHGT PSQTTAKNWE LTASASHQPP GVYPQGHSDT TVAISTSTVL
LCGLSAVSLL ACYLKSRQTP LLASVEMEAM EALPVTWGTS SRDEDLENCS HHL*

Position of stopcodon in wt / mu CDS

1062 / 1062

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

354 / 354

Position of stopcodon in wt / mu cDNA

1076 / 1076

Position of start ATG in wt / mu cDNA

15 / 15

Last intron/exon boundary

964

Theoretical NMD boundary in CDS

899

Length of CDS

1062

Coding sequence (CDS) position

962

cDNA position

976

gDNA position

24993

Chromosomal position

5953195

Speed

0.38 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:

10:5953195G>A_2_ENST00000528354

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 56|44 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.37, LOF (oe): 0.93, misssense (oe): 1.01, synonymous (oe): 1.15 ? (gnomAD)

Ensembl transcript ID

ENST00000528354.5

Genbank transcript ID

NM_172200 (by similarity)

UniProt / AlphaMissense peptide

I15RA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.605C>T
g.24993C>T

AA changes

AAE:	P202L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

Species	Match	AA	Alignment
Human		202	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A	L
mutated	not conserved	202	L	A	C	Y	L	K	S	R	Q	T	P	L	L	A	S	V	E	M	E	A	M	E	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
31	205	TOPO_DOM	Extracellular	lost
31	267	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRG ITCPPPMSVE HADIWVKSYS LYSRERYICN
SGFKRKAGTS SLTECVLNKA TNVAHWTTPS LKCIKPAASS PSSNNTAATT AAIVPGSQLM
PSKSPSTGTT EISSHESSHG TPSQTTAKNW ELTASASHQP PGVYPQGHSD TTVAISTSTV
LLCGLSAVSL LACYLKSRQT PPLASVEMEA MEALPVTWGT SSRDEDLENC SHHL*

Mutated AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRG ITCPPPMSVE HADIWVKSYS LYSRERYICN
SGFKRKAGTS SLTECVLNKA TNVAHWTTPS LKCIKPAASS PSSNNTAATT AAIVPGSQLM
PSKSPSTGTT EISSHESSHG TPSQTTAKNW ELTASASHQP PGVYPQGHSD TTVAISTSTV
LLCGLSAVSL LACYLKSRQT PLLASVEMEA MEALPVTWGT SSRDEDLENC SHHL*

Position of stopcodon in wt / mu CDS

705 / 705

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

235 / 235

Position of stopcodon in wt / mu cDNA

735 / 735

Position of start ATG in wt / mu cDNA

31 / 31

Last intron/exon boundary

623

Theoretical NMD boundary in CDS

542

Length of CDS

705

Coding sequence (CDS) position

605

cDNA position

635

gDNA position

24993

Chromosomal position

5953195

Speed

0.36 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:

10:5953195G>A_1_ENST00000620345

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.44, LOF (oe): 0.99, misssense (oe): 1.04, synonymous (oe): 1.15 ? (gnomAD)

Ensembl transcript ID

ENST00000620345.4

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.845+3184C>T
g.24993C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

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

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRD ARDRLAVLAG RSRISESFNH EVQTHEACVR
LRTMENCPQC HHHRTSRQQA GITCPPPMSV EHADIWVKSY SLYSRERYIC NSGFKRKAGT
SSLTECVLNK ATNVAHWTTP SLKCIRDPAL VHQRPAPPST VTTAGVTPQP ESLSPSGKEP
AASSPSSNNT AATTAAIVPG SQLMPSKSPS TGTTEISSHE SSHGTPSQTT AKNWELTASA
SHQPPGVYPQ GHSDTTVAIS TSTVLLCGLS AVSLLACYLK SRWLAKRSLP GDAEAPNMSR
GGRNAWEQLS RAPATSLLRT PVESALSASR P*

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

120 / 120

Last intron/exon boundary

964

Theoretical NMD boundary in CDS

794

Length of CDS

996

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

24993

Chromosomal position

5953195

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:

10:5953195G>A_5_ENST00000397251

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 0|200 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.43, LOF (oe): 0.99, misssense (oe): 1.04, synonymous (oe): 1.15 ? (gnomAD)

Ensembl transcript ID

ENST00000397251.7

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.846-2371C>T
g.24993C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

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

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRD ARDRLAVLAG RSRISESFNH EVQTHEACVR
LRTMENCPQC HHHRTSRQQA GITCPPPMSV EHADIWVKSY SLYSRERYIC NSGFKRKAGT
SSLTECVLNK ATNVAHWTTP SLKCIRDPAL VHQRPAPPST VTTAGVTPQP ESLSPSGKEP
AASSPSSNNT AATTAAIVPG SQLMPSKSPS TGTTEISSHE SSHGTPSQTT AKNWELTASA
SHQPPGVYPQ GHSDTTVAIS TSTVLLCGLS AVSLLACYLK SSLDAFIKIR GGFSTWLLGL
PHSTVGSG*

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

120 / 120

Last intron/exon boundary

964

Theoretical NMD boundary in CDS

794

Length of CDS

927

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

24993

Chromosomal position

5953195

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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MutationT@ster 2025

Variant:

10:5953195G>A_4_ENST00000379971

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Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.08, LOF (oe): 0.58, misssense (oe): 1.06, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000379971.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.545C>T
g.24993C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

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

polyA signal ok

AA sequence altered

N/A

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRE PAASSPSSNN TAATTAAIVP GSQLMPSKSP
STGTTEISSH ESSHGTPSQT TAKNWELTAS ASHQPPGVYP QGHSDTTVAI STSTVLLCGL
SAVSLLACYL KSRASVCSCH PRSAGHTCSV GSVC*

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

16 / 16

Last intron/exon boundary

413

Theoretical NMD boundary in CDS

347

Length of CDS

465

Coding sequence (CDS) position

N/A

cDNA position

545

gDNA position

24993

Chromosomal position

5953195

Speed

0.37 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:

10:5953195G>A_8_ENST00000379977

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 29|71 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:5953195G>A (GRCh38)

Gene symbol

IL15RA

Gene constraints

LOEUF: 1.46, LOF (oe): 1.02, misssense (oe): 1.02, synonymous (oe): 1.15 ? (gnomAD)

Ensembl transcript ID

ENST00000379977.8

Genbank transcript ID

NM_002189 (exact from MANE)

UniProt / AlphaMissense peptide

I15RA_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.704C>T
g.24993C>T

AA changes

AAE:	P235L	?
Score:	98

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs147420996
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	1	148	149

Protein conservation

Species	Match	AA	Alignment
Human		235	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A	L
mutated	not conserved	235	L	A	C	Y	L	K	S	R	Q	T	P	L	L	A	S	V	E
Ptroglodytes	all identical	321	L	A	C	Y	L	K	S	R	Q	T	P	P	L	A	S	V	E	M	E	A	M	E	A
Mmulatta	all identical	240	L	A	C	Y	I	K	S	R	Q	T	P	P	P	A	S	I	E	M	E	A	M	E	A
Fcatus	not conserved	236	L	V	C	Y	K	R	S	R	Q	T	S	Q	I	R	T	V	A	M	E	N	M	E	E
Mmusculus	not conserved	235	L	A	W	Y	I	K	S	R	Q	P	S	Q	P	C
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
31	267	CHAIN		lost
229	267	TOPO_DOM	Cytoplasmic	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.112	0
	-1.148	0
(flanking)	1.338	0.003

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

10

Strand

-1

Original gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered gDNA sequence snippet

GCTTTGCAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Original cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCCGCTGGCCAGCGTTGAAATGG

Altered cDNA sequence snippet

CAAGTCAAGGCAAACTCCCCTGCTGGCCAGCGTTGAAATGG

Wildtype AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRG ITCPPPMSVE HADIWVKSYS LYSRERYICN
SGFKRKAGTS SLTECVLNKA TNVAHWTTPS LKCIRDPALV HQRPAPPSTV TTAGVTPQPE
SLSPSGKEPA ASSPSSNNTA ATTAAIVPGS QLMPSKSPST GTTEISSHES SHGTPSQTTA
KNWELTASAS HQPPGVYPQG HSDTTVAIST STVLLCGLSA VSLLACYLKS RQTPPLASVE
MEAMEALPVT WGTSSRDEDL ENCSHHL*

Mutated AA sequence

MAPRRARGCR TLGLPALLLL LLLRPPATRG ITCPPPMSVE HADIWVKSYS LYSRERYICN
SGFKRKAGTS SLTECVLNKA TNVAHWTTPS LKCIRDPALV HQRPAPPSTV TTAGVTPQPE
SLSPSGKEPA ASSPSSNNTA ATTAAIVPGS QLMPSKSPST GTTEISSHES SHGTPSQTTA
KNWELTASAS HQPPGVYPQG HSDTTVAIST STVLLCGLSA VSLLACYLKS RQTPLLASVE
MEAMEALPVT WGTSSRDEDL ENCSHHL*

Position of stopcodon in wt / mu CDS

804 / 804

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

268 / 268

Position of stopcodon in wt / mu cDNA

855 / 855

Position of start ATG in wt / mu cDNA

52 / 52

Last intron/exon boundary

743

Theoretical NMD boundary in CDS

641

Length of CDS

804

Coding sequence (CDS) position

704

cDNA position

755

gDNA position

24993

Chromosomal position

5953195

Speed

0.38 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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