MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000302450
MT speed 0.59 s - this script 3.056454 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000302450(MANE Select)	CKAP2L	Deleterious	66\|34	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

2:112762530T>C_1_ENST00000302450

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 66|34 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr2:112762530T>C (GRCh38)

Gene symbol

CKAP2L

Gene constraints

LOEUF: 0.72, LOF (oe): 0.53, misssense (oe): 1.00, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000302450.11

Genbank transcript ID

NM_152515 (exact from MANE), NM_001304361 (by similarity)

UniProt / AlphaMissense peptide

CKP2L_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.77A>G
g.2135A>G

AA changes

AAE:	K26R	?
Score:	26

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs35593767
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	9	1061	1070

Protein conservation

Species	Match	AA	Alignment
Human		26	R	Q	R	K	L	Q	E	Y	L	A	A	K	G	K	L	K	S	Q	N	T	K	P	Y	L
mutated	all conserved	26	R	Q	R	K	L	Q	E	Y	L	A	A	R	G	K	L	K	S	Q	N	T	K	P	Y
Ptroglodytes	all identical	26	R	Q	R	K	L	Q	E	Y	L	A	A	K	G	K	L	K	S	Q	N	T	K	P	Y
Mmulatta	all identical	26	R	Q	R	K	L	Q	E	Y	L	A	A	K	G	K	L	R	S	Q	N	T	K	P	Y
Fcatus	all identical	26	R	Q	R	K	L	Q	E	Y	L	A	A	K	G	K	L	K	C	Q	N	T	K	P	Y
Mmusculus	all identical	26	R	W	Q	K	L	Q	E	Y	L	A	A	K	G	K	L	K	D	P	N	A	K	P	Y
Ggallus	all identical	507	R	R	R	Q	L	Q	E	Y	L	E	A	K	G	K	L	K	C	P	S	T	K	A	Y
Trubripes	all identical	26	H	K	Q	K	L	M	E	Y	L	K	A	K	G	K	F	K	V	P	T	T	K	P	N
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	54	R	R	R	Q	L	Q	E	Y	L	A	A	K	G	K	L	K	PL	T	N	T	K	P	Y

Protein features

Start (aa)	End (aa)	Feature	Details
1	745	CHAIN		lost
25	141	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.263	0.999
	3.719	1
(flanking)	3.719	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

2

Strand

-1

Original gDNA sequence snippet

TCAGGAGTACCTTGCAGCCAAGGGAAAACTGAAGAGCCAAA

Altered gDNA sequence snippet

TCAGGAGTACCTTGCAGCCAGGGGAAAACTGAAGAGCCAAA

Original cDNA sequence snippet

TCAGGAGTACCTTGCAGCCAAGGGAAAACTGAAGAGCCAAA

Altered cDNA sequence snippet

TCAGGAGTACCTTGCAGCCAGGGGAAAACTGAAGAGCCAAA

Wildtype AA sequence

MVGPGPTAAA AVEERQRKLQ EYLAAKGKLK SQNTKPYLKS KNNCQNQPPS KSTIRPKNDV
TNHVVLPVKP KRSISIKLQP RPPNTAGSQK PKLEPPKLLG KRLTSECVSS NPYSKPSSKS
FQQCEAGSST TGELSRKPVG SLNIEQLKTT KQQLTDQGNG KCIDFMNNIH VENESLDNFL
KETNKENLLD ILTEPERKPD PKLYTRSKPK TDSYNQTKNS LVPKQALGKS SVNSAVLKDR
VNKQFVGETQ SRTFPVKSQQ LSRGADLARP GVKPSRTVPS HFIRTLSKVQ SSKKPVVKNI
KDIKVNRSQY ERPNETKIRS YPVTEQRVKH TKPRTYPSLL QGEYNNRHPN IKQDQKSSQV
CIPQTSCVLQ KSKAISQRPN LTVGRFNSAI PSTPSIRPNG TSGNKHNNNG FQQKAQTLDS
KLKKAVPQNH FLNKTAPKTQ ADVTTVNGTQ TNPNIKKKAT AEDRRKQLEE WQKSKGKTYK
RPPMELKTKR KVIKEMNISF WKSIEKEEEE KKAQLELSSK INNTLTECLN LIEGGVPSNE
ILNILSSIPE AEKFAKFWIC KAKLLASKGT FDVIGLYEEA IKNGATPIQE LRKVVLNILQ
DSNRTTEGIT SDSLVAETSI TSVEELAKKM ESVKSCLSPK EREQVTATPR IAKAEQHNYP
GIKLQIGPIP RINGMPEVQD MKFITPVRRS SRIERAVSRY PEMLQEHDLV VASLDELLEV
EETKCFIFRR NEALPVTLGF QTPES*

Mutated AA sequence

MVGPGPTAAA AVEERQRKLQ EYLAARGKLK SQNTKPYLKS KNNCQNQPPS KSTIRPKNDV
TNHVVLPVKP KRSISIKLQP RPPNTAGSQK PKLEPPKLLG KRLTSECVSS NPYSKPSSKS
FQQCEAGSST TGELSRKPVG SLNIEQLKTT KQQLTDQGNG KCIDFMNNIH VENESLDNFL
KETNKENLLD ILTEPERKPD PKLYTRSKPK TDSYNQTKNS LVPKQALGKS SVNSAVLKDR
VNKQFVGETQ SRTFPVKSQQ LSRGADLARP GVKPSRTVPS HFIRTLSKVQ SSKKPVVKNI
KDIKVNRSQY ERPNETKIRS YPVTEQRVKH TKPRTYPSLL QGEYNNRHPN IKQDQKSSQV
CIPQTSCVLQ KSKAISQRPN LTVGRFNSAI PSTPSIRPNG TSGNKHNNNG FQQKAQTLDS
KLKKAVPQNH FLNKTAPKTQ ADVTTVNGTQ TNPNIKKKAT AEDRRKQLEE WQKSKGKTYK
RPPMELKTKR KVIKEMNISF WKSIEKEEEE KKAQLELSSK INNTLTECLN LIEGGVPSNE
ILNILSSIPE AEKFAKFWIC KAKLLASKGT FDVIGLYEEA IKNGATPIQE LRKVVLNILQ
DSNRTTEGIT SDSLVAETSI TSVEELAKKM ESVKSCLSPK EREQVTATPR IAKAEQHNYP
GIKLQIGPIP RINGMPEVQD MKFITPVRRS SRIERAVSRY PEMLQEHDLV VASLDELLEV
EETKCFIFRR NEALPVTLGF QTPES*

Position of stopcodon in wt / mu CDS

2238 / 2238

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

746 / 746

Position of stopcodon in wt / mu cDNA

2249 / 2249

Position of start ATG in wt / mu cDNA

12 / 12

Last intron/exon boundary

2023

Theoretical NMD boundary in CDS

1961

Length of CDS

2238

Coding sequence (CDS) position

77

cDNA position

88

gDNA position

2135

Chromosomal position

112762530

Speed

0.59 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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