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: ENST00000254035
Querying Taster for transcript #2: ENST00000424301
Querying Taster for transcript #3: ENST00000437669
MT speed 0.19 s - this script 2.586943 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
ENST00000254035(MANE Select)	CKMT2	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000424301	CKMT2	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000437669	CKMT2	Deleterious	96\|4	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

5:81255059C>T_1_ENST00000254035

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:81255059C>T (GRCh38)

Gene symbol

CKMT2

Gene constraints

LOEUF: 1.07, LOF (oe): 0.79, misssense (oe): 0.81, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000254035.9

Genbank transcript ID

NM_001099735 (exact from MANE)

UniProt / AlphaMissense peptide

KCRS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.514C>T
g.21740C>T

AA changes

AAE:	R172C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376567528
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	24	24

Protein conservation

Species	Match	AA	Alignment
Human		172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C	T	R	A	E
mutated	not conserved	172	L	S	S	R	V	R	T	G	R	S	I	C	G	L	S	L	P	P	A	C
Ptroglodytes	all identical	172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Mmulatta	all identical	246	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Fcatus	all identical	196	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Mmusculus	all identical	172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Ggallus	all identical	172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Trubripes	all identical	170	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C
Drerio	no homologue
Dmelanogaster	all conserved	337	I	S	T	R	V	R	C	G	R	S	M	Q	G	Y	P	F	N	P	C	L	T	E	A
Celegans	all conserved	968	N	S	T	R	I	R	C	G	R	S	L	Q	G
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
40	419	CHAIN		lost
159	401	DOMAIN	Phosphagen kinase C-terminal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.995	1
	5.699	1
(flanking)	9.557	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

5

Strand

1

Original gDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered gDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Original cDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered cDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Wildtype AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS IRGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Mutated AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS ICGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Position of stopcodon in wt / mu CDS

1260 / 1260

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

420 / 420

Position of stopcodon in wt / mu cDNA

1336 / 1336

Position of start ATG in wt / mu cDNA

77 / 77

Last intron/exon boundary

1216

Theoretical NMD boundary in CDS

1089

Length of CDS

1260

Coding sequence (CDS) position

514

cDNA position

590

gDNA position

21740

Chromosomal position

81255059

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

Back to summary table

MutationT@ster 2025

Variant:

5:81255059C>T_2_ENST00000424301

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:81255059C>T (GRCh38)

Gene symbol

CKMT2

Gene constraints

LOEUF: 1.07, LOF (oe): 0.79, misssense (oe): 0.81, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000424301.6

Genbank transcript ID

NM_001825 (by similarity)

UniProt / AlphaMissense peptide

KCRS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.514C>T
g.21740C>T

AA changes

AAE:	R172C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376567528
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	24	24

Protein conservation

Species	Match	AA	Alignment
Human		172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C	T	R	A	E
mutated	not conserved	172	L	S	S	R	V	R	T	G	R	S	I	C	G	L	S	L	P	P	A	C
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
40	419	CHAIN		lost
159	401	DOMAIN	Phosphagen kinase C-terminal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.995	1
	5.699	1
(flanking)	9.557	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

5

Strand

1

Original gDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered gDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Original cDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered cDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Wildtype AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS IRGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Mutated AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS ICGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Position of stopcodon in wt / mu CDS

1260 / 1260

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

420 / 420

Position of stopcodon in wt / mu cDNA

1498 / 1498

Position of start ATG in wt / mu cDNA

239 / 239

Last intron/exon boundary

1378

Theoretical NMD boundary in CDS

1089

Length of CDS

1260

Coding sequence (CDS) position

514

cDNA position

752

gDNA position

21740

Chromosomal position

81255059

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:

5:81255059C>T_3_ENST00000437669

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr5:81255059C>T (GRCh38)

Gene symbol

CKMT2

Gene constraints

LOEUF: 1.07, LOF (oe): 0.79, misssense (oe): 0.81, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000437669.5

Genbank transcript ID

NM_001099736 (by similarity)

UniProt / AlphaMissense peptide

KCRS_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.514C>T
g.21740C>T

AA changes

AAE:	R172C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs376567528
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	24	24

Protein conservation

Species	Match	AA	Alignment
Human		172	L	S	S	R	V	R	T	G	R	S	I	R	G	L	S	L	P	P	A	C	T	R	A	E
mutated	not conserved	172	L	S	S	R	V	R	T	G	R	S	I	C	G	L	S	L	P	P	A	C
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
40	419	CHAIN		lost
159	401	DOMAIN	Phosphagen kinase C-terminal	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.995	1
	5.699	1
(flanking)	9.557	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

5

Strand

1

Original gDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered gDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Original cDNA sequence snippet

TGCGCACTGGCCGCAGCATCCGTGGGCTGAGCCTGCCTCCA

Altered cDNA sequence snippet

TGCGCACTGGCCGCAGCATCTGTGGGCTGAGCCTGCCTCCA

Wildtype AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS IRGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Mutated AA sequence

MASIFSKLLT GRNASLLFAT MGTSVLTTGY LLNRQKVCAE VREQPRLFPP SADYPDLRKH
NNCMAECLTP AIYAKLRNKV TPNGYTLDQC IQTGVDNPGH PFIKTVGMVA GDEESYEVFA
DLFDPVIKLR HNGYDPRVMK HTTDLDASKI TQGQFDEHYV LSSRVRTGRS ICGLSLPPAC
TRAERREVEN VAITALEGLK GDLAGRYYKL SEMTEQDQQR LIDDHFLFDK PVSPLLTCAG
MARDWPDARG IWHNYDKTFL IWINEEDHTR VISMEKGGNM KRVFERFCRG LKEVERLIQE
RGWEFMWNER LGYILTCPSN LGTGLRAGVH VRIPKLSKDP RFSKILENLR LQKRGTGGVD
TAAVADVYDI SNIDRIGRSE VELVQIVIDG VNYLVDCEKK LERGQDIKVP PPLPQFGKK*

Position of stopcodon in wt / mu CDS

1260 / 1260

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

420 / 420

Position of stopcodon in wt / mu cDNA

1342 / 1342

Position of start ATG in wt / mu cDNA

83 / 83

Last intron/exon boundary

1222

Theoretical NMD boundary in CDS

1089

Length of CDS

1260

Coding sequence (CDS) position

514

cDNA position

596

gDNA position

21740

Chromosomal position

81255059

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