MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.80, LOF (oe): 1.26, misssense (oe): 1.00, synonymous (oe): 0.74 ? (gnomAD)

Ensembl transcript ID

ENST00000464581.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.440delC
g.46554delC

AA changes

T147Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		147	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	147	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MERLLYGIGA CGEVKLAFER KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL
NHPCIIKIKN FFDAEDYYIV LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE
NGIIHRDLKP ENVLLSSQEE DCLIKITDFG HSKILGETSL MRTLCGTPTY LAPEVLVSVG
TAGYNRAVDC WSLGVILFIC LSGYPPFSEH RTQVSLKDQI TSGKYNFIPE VWAEVSEKAL
DLVKKLLVVD PKARFTTEEA LRHPWLQDED MKRKFQDLLS EENESTALPQ VLAQPSTSRK
RPREGEAEGA ETTKRPAVCA AVL*

Mutated AA sequence

MERLLYGIGA CGEVKLAFER KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL
NHPCIIKIKN FFDAEDYYIV LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE
NGIIHRDLKP ENVLLSSQEE DCLIKIMILG TPRFWERPLS *

Position of stopcodon in wt / mu CDS

972 / 483

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

324 / 161

Position of stopcodon in wt / mu cDNA

984 / 495

Position of start ATG in wt / mu cDNA

13 / 13

Last intron/exon boundary

894

Theoretical NMD boundary in CDS

831

Length of CDS

972

Coding sequence (CDS) position

439 / 441

cDNA position

451 / 453

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.25 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:

22:28695868AG>A_2_ENST00000402731

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.51, LOF (oe): 1.15, misssense (oe): 0.99, synonymous (oe): 0.78 ? (gnomAD)

Ensembl transcript ID

ENST00000402731.6

Genbank transcript ID

NM_001349956 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Deletion

Gene region

CDS

DNA changes

c.899delC
g.46554delC

AA changes

T300Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		300	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	300	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREE NLSCPYRIWF NGACGEVKLA FERKTCKKVA
IKIISKRKFA IGSAREADPA LNVETEIEIL KKLNHPCIIK IKNFFDAEDY YIVLELMEGG
ELFDKVVGNK RLKEATCKLY FYQMLLAVQY LHENGIIHRD LKPENVLLSS QEEDCLIKIT
DFGHSKILGE TSLMRTLCGT PTYLAPEVLV SVGTAGYNRA VDCWSLGVIL FICLSGYPPF
SEHRTQVSLK DQITSGKYNF IPEVWAEVSE KALDLVKKLL VVDPKARFTT EEALRHPWLQ
DEDMKRKFQD LLSEENESTA LPQVLAQPST SRKRPREGEA EGAETTKRPA VCAAVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREE NLSCPYRIWF NGACGEVKLA FERKTCKKVA
IKIISKRKFA IGSAREADPA LNVETEIEIL KKLNHPCIIK IKNFFDAEDY YIVLELMEGG
ELFDKVVGNK RLKEATCKLY FYQMLLAVQY LHENGIIHRD LKPENVLLSS QEEDCLIKIM
ILGTPRFWER PLS*

Position of stopcodon in wt / mu CDS

1431 / 942

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

477 / 314

Position of stopcodon in wt / mu cDNA

1437 / 948

Position of start ATG in wt / mu cDNA

7 / 7

Last intron/exon boundary

1347

Theoretical NMD boundary in CDS

1290

Length of CDS

1431

Coding sequence (CDS) position

898 / 900

cDNA position

904 / 906

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.31 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:

22:28695868AG>A_3_ENST00000425190

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.80, LOF (oe): 1.26, misssense (oe): 1.00, synonymous (oe): 0.74 ? (gnomAD)

Ensembl transcript ID

ENST00000425190.7

Genbank transcript ID

NM_001257387 (by similarity)

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.437delC
g.46554delC

AA changes

T146Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		146	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	146	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
113	175	DOMAIN	FHA	lost
144	150	STRAND		lost
154	162	STRAND		lost
168	170	STRAND		lost
180	182	STRAND		lost
187	193	STRAND		lost
197	203	STRAND		lost
209	211	HELIX		lost
214	219	HELIX		lost
220	228	STRAND		lost
220	486	DOMAIN	Protein kinase	lost
227	234	BINDING	ATP	lost
230	239	STRAND		lost
240	243	TURN		lost
244	251	STRAND		lost
249	249	BINDING	ATP	lost
253	256	HELIX		lost
270	279	HELIX		lost
288	302	STRAND		lost
302	308	BINDING	ATP	lost
307	309	STRAND		lost
310	313	HELIX		lost
314	316	HELIX		lost
321	340	HELIX		lost
347	347	ACT_SITE		lost
350	352	HELIX		lost
351	352	BINDING	ATP	lost
353	361	STRAND		lost
364	366	STRAND		lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE TEIEILKKLN
HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM LLAVQYLHEN
GIIHRDLKPE NVLLSSQEED CLIKITDFGH SKILGETSLM RTLCGTPTYL APEVLVSVGT
AGYNRAVDCW SLGVILFICL SGYPPFSEHR TQVSLKDQIT SGKYNFIPEV WAEVSEKALD
LVKKLLVVDP KARFTTEEAL RHPWLQDEDM KRKFQDLLSE ENESTALPQV LAQPSTSRKR
PREGEAEGAE TTKRPAVCAA VL*

Mutated AA sequence

MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE TEIEILKKLN
HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM LLAVQYLHEN
GIIHRDLKPE NVLLSSQEED CLIKIMILGT PRFWERPLS*

Position of stopcodon in wt / mu CDS

969 / 480

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

323 / 160

Position of stopcodon in wt / mu cDNA

1356 / 867

Position of start ATG in wt / mu cDNA

388 / 388

Last intron/exon boundary

1266

Theoretical NMD boundary in CDS

828

Length of CDS

969

Coding sequence (CDS) position

436 / 438

cDNA position

823 / 825

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.30 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:

22:28695868AG>A_5_ENST00000649563

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.80, LOF (oe): 1.26, misssense (oe): 1.00, synonymous (oe): 0.74 ? (gnomAD)

Ensembl transcript ID

ENST00000649563.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.437delC
g.46554delC

AA changes

T146Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		146	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	146	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
113	175	DOMAIN	FHA	lost
144	150	STRAND		lost
154	162	STRAND		lost
168	170	STRAND		lost
180	182	STRAND		lost
187	193	STRAND		lost
197	203	STRAND		lost
209	211	HELIX		lost
214	219	HELIX		lost
220	228	STRAND		lost
220	486	DOMAIN	Protein kinase	lost
227	234	BINDING	ATP	lost
230	239	STRAND		lost
240	243	TURN		lost
244	251	STRAND		lost
249	249	BINDING	ATP	lost
253	256	HELIX		lost
270	279	HELIX		lost
288	302	STRAND		lost
302	308	BINDING	ATP	lost
307	309	STRAND		lost
310	313	HELIX		lost
314	316	HELIX		lost
321	340	HELIX		lost
347	347	ACT_SITE		lost
350	352	HELIX		lost
351	352	BINDING	ATP	lost
353	361	STRAND		lost
364	366	STRAND		lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE TEIEILKKLN
HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM LLAVQYLHEN
GIIHRDLKPE NVLLSSQEED CLIKITDFGH SKILGETSLM RTLCGTPTYL APEVLVSVGT
AGYNRAVDCW SLGVILFICL SGYPPFSEHR TQVSLKDQIT SGKYNFIPEV WAEVSEKALD
LVKKLLVVDP KARFTTEEAL RHPWLQDEDM KRKFQDLLSE ENESTALPQV LAQPSTSRKR
PREGEAEGAE TTKRPAVCAA VL*

Mutated AA sequence

MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE TEIEILKKLN
HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM LLAVQYLHEN
GIIHRDLKPE NVLLSSQEED CLIKIMILGT PRFWERPLS*

Position of stopcodon in wt / mu CDS

969 / 480

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

323 / 160

Position of stopcodon in wt / mu cDNA

1078 / 589

Position of start ATG in wt / mu cDNA

110 / 110

Last intron/exon boundary

988

Theoretical NMD boundary in CDS

828

Length of CDS

969

Coding sequence (CDS) position

436 / 438

cDNA position

545 / 547

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

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:

22:28695868AG>A_6_ENST00000405598

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.40, LOF (oe): 1.07, misssense (oe): 1.00, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000405598.5

Genbank transcript ID

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1100delC
g.46554delC

AA changes

T367Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		367	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	367						D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKITDFG HSKILGETSL MRTLCGTPTY LAPEVLVSVG TAGYNRAVDC WSLGVILFIC
LSGYPPFSEH RTQVSLKDQI TSGKYNFIPE VWAEVSEKAL DLVKKLLVVD PKARFTTEEA
LRHPWLQDED MKRKFQDLLS EENESTALPQ VLAQPSTSRK RPREGEAEGA ETTKRPAVCA
AVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKIMILG TPRFWERPLS *

Position of stopcodon in wt / mu CDS

1632 / 1143

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

544 / 381

Position of stopcodon in wt / mu cDNA

1824 / 1335

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1734

Theoretical NMD boundary in CDS

1491

Length of CDS

1632

Coding sequence (CDS) position

1099 / 1101

cDNA position

1291 / 1293

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.30 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:

22:28695868AG>A_7_ENST00000382580

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.40, LOF (oe): 1.07, misssense (oe): 1.00, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000382580.6

Genbank transcript ID

NM_001005735 (by similarity)

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1229delC
g.46554delC

AA changes

T410Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		410	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	410	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLETES GHVTQSDLEL
LLSSDPPASA SQSAGIRGVR HHPRPVCSLK CVNDNYWFGR DKSCEYCFDE PLLKRTDKYR
TYSKKHFRIF REVGPKNSYI AYIEDHSGNG TFVNTELVGK GKRRPLNNNS EIALSLSRNK
VFVFFDLTVD DQSVYPKALR DEYIMSKTLG SGACGEVKLA FERKTCKKVA IKIISKRKFA
IGSAREADPA LNVETEIEIL KKLNHPCIIK IKNFFDAEDY YIVLELMEGG ELFDKVVGNK
RLKEATCKLY FYQMLLAVQY LHENGIIHRD LKPENVLLSS QEEDCLIKIT DFGHSKILGE
TSLMRTLCGT PTYLAPEVLV SVGTAGYNRA VDCWSLGVIL FICLSGYPPF SEHRTQVSLK
DQITSGKYNF IPEVWAEVSE KALDLVKKLL VVDPKARFTT EEALRHPWLQ DEDMKRKFQD
LLSEENESTA LPQVLAQPST SRKRPREGEA EGAETTKRPA VCAAVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLETES GHVTQSDLEL
LLSSDPPASA SQSAGIRGVR HHPRPVCSLK CVNDNYWFGR DKSCEYCFDE PLLKRTDKYR
TYSKKHFRIF REVGPKNSYI AYIEDHSGNG TFVNTELVGK GKRRPLNNNS EIALSLSRNK
VFVFFDLTVD DQSVYPKALR DEYIMSKTLG SGACGEVKLA FERKTCKKVA IKIISKRKFA
IGSAREADPA LNVETEIEIL KKLNHPCIIK IKNFFDAEDY YIVLELMEGG ELFDKVVGNK
RLKEATCKLY FYQMLLAVQY LHENGIIHRD LKPENVLLSS QEEDCLIKIM ILGTPRFWER
PLS*

Position of stopcodon in wt / mu CDS

1761 / 1272

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

587 / 424

Position of stopcodon in wt / mu cDNA

1837 / 1348

Position of start ATG in wt / mu cDNA

77 / 77

Last intron/exon boundary

1747

Theoretical NMD boundary in CDS

1620

Length of CDS

1761

Coding sequence (CDS) position

1228 / 1230

cDNA position

1304 / 1306

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.30 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:

22:28695868AG>A_4_ENST00000404276

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.40, LOF (oe): 1.07, misssense (oe): 1.00, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000404276.6

Genbank transcript ID

NM_007194 (exact from MANE)

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1100delC
g.46554delC

AA changes

T367Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		367	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	V	S	V	G	T	A	G	Y	N	R	A	V	D	C	W	S	L	G	V	I	L	F	I	C	L	S	G	Y	P	P	F	S	E	H	R	T	Q	V	S	L	K	D	Q	I	T	S	G	K	Y	N	F	I	P	E	V	W	A	E	V	S	E	K	A	L	D	L	V	K	K	L	L	V	V	D	P	K	A	R	F	T	T	E	E	A	L	R	H	P	W	L	Q	D	E	D	M	K	R
mutated	partly conserved	367						D	C	L	I	K	I	M	I	L	G
Ptroglodytes	all identical	410	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	V	S	V	G	T	A	G	Y	N	R	A	V	D	C	W	S	L	G	V	I	L	F	I	C	L	S	G	Y	P	P	F	S	E	H	R	T	Q	V	S	L	K
Mmulatta	all identical	367						D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	V	S	V	G	T	A	G	Y	N	R	A	V	D	C	W	S	L	G	V	I	L	F	I	C	L	S	G	Y	P	P	F	S	E	H	R	T	Q	V	S	L	K	D	Q	I	T	S	G	K	Y	N	F	I	P	E	V	W	A	E	V	S	E	K	A	L	D	L	V	K	K	L	L	V	V	D	P	K	A	R	F	T	T	E	E	A
Fcatus	partly conserved	393	S	S	Q	K	E	D	C	L	I	K	I	T	D	F	G	Q	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	N	S	F	G	T	A	G	Y	N	R	A	V	D	C	W	S	L	G	V	I	L	F	I	C	L	S	G	Y	P	P	F	S	E	H	K	T	Q	V	S	L	K	D	Q	I	T	S	G	K	F	N	F	I	P	E	V	W	A	E	V	S	E	K	A	L	D	L	V	K	K	L	L	I	V	D	P	K	V
Mmusculus	partly conserved	371								L	I	K	I	T	D	F	G	Q	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	V	S	N	G	T	A	G	Y	S	R	A	V	D	C	W	S	L	G	V	I	L	F	I	C	L	S	G	Y	P	P	F	S	E	H	K	T	Q	V	S	L	K	D	Q	I	T	S	G	K	Y	N	F	I	P	E	V	W	T	D	V	S	E	E	A	L	D	L	V	K	K	L	L	V	V	D	P	K	A	R	L	T	T	E	E	A	L	N
Ggallus	partly conserved	344						T	C	L	I	K	I	T	D	F	G	Q	S	K	I	L	G	E	T	S	L	M	K	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	N	S	F	G	T	A	G	Y	S	R	A	V	D	C	W	S	L	G	V	I	L	F	V	C	L	C	G	Y	P	P	F	N	E	Q	N	T	Q	L	S	L	K	D	Q	I	T	R	G	E	Y	T	F	I	S	K	E	W	K	H	V	S	N	M	A	L	D	L	V	K	K	L	L	V	V	D	P	S	K	R	F	T	I	E	E	A
Trubripes	partly conserved	346			Q	E	D	I	C	L	I	K	V	T	D	F	N	Q	S	R	I	L	E	E	T	M	L	M	R	T	L	C	G	T	P	S	Y	L	A	P	E	V	F	T	Q	A	S	T	T	G	Y	S	L	A	V	D	A	W	S	L	G	V	L	L	F	V	C	L	G	G	Y	P	P	F	H	E	G	F	G	N	L	S	I	T	E	Q	I	I	R	G	E	F	T	M	V	P	S	K	W	K	H	I	S	D	Q	A	K	D	V	V	R	K	L	L	V	V	D	P	S	K	R	M	S	I
Drerio	no homologue
Dmelanogaster	partly conserved	323	E	T	N	D	E	E	T	L	L	K	V	S	D	F	G	L	S	K	F	V	Q	K	D	S	V	M	R	T	L	C	G	T	P	L	Y	V	A	P	E	V	L	I	T	G	G	R	E	A	Y	T	K	K	V	D	I	W	S	L	G	V	V	L	F	T	C	L	S	G	T	L	P	F	S	D	E	Y	G	T	P	A	A
Celegans	partly conserved	790									L	K	L	T	D	F	G	M	A	K	-	-	N	S	V	N	R	M	K	T	R	C	G	T	P	S	Y	N	A	P	E	I	V	A	N	E	G	V	E	-	Y	T	P	K	V	D	I	W	S	L	G	C	V	L	F	I	T	F	S	G	Y	P	P	F	S	E	E	Y	T	D	M	T	M	D	E	Q	V	L	T	G	R	L	I	F	H	A	Q	-	W	R	R	I	T	V	E	T	Q	N	M	I	K	W	M	L	T	V	E	P	S	N	R	P	S	A	V	E	L	M	S	T
Xtropicalis	partly conserved	408	S	S	S	N	E	E	C	C	I	K	I	T	D	F	G	Q	S	K	I	L	G	E	T	S	L	M	R	T	L	C	G	T	P	T	Y	L	A	P	E	V	L	N	T	A	G	T	T	G	Y	S	R	A	V	D	Y	W	S	L	G	V	I	L	F	V	C	L	S	G	Y	P	P	F	S	E	Q	N	S	K	I	P	L	K	N	Q	I	A	E	G	K	Y	T	Y	I	P	A	A	W	D	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKITDFG HSKILGETSL MRTLCGTPTY LAPEVLVSVG TAGYNRAVDC WSLGVILFIC
LSGYPPFSEH RTQVSLKDQI TSGKYNFIPE VWAEVSEKAL DLVKKLLVVD PKARFTTEEA
LRHPWLQDED MKRKFQDLLS EENESTALPQ VLAQPSTSRK RPREGEAEGA ETTKRPAVCA
AVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKIMILG TPRFWERPLS *

Position of stopcodon in wt / mu CDS

1632 / 1143

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

544 / 381

Position of stopcodon in wt / mu cDNA

1690 / 1201

Position of start ATG in wt / mu cDNA

59 / 59

Last intron/exon boundary

1600

Theoretical NMD boundary in CDS

1491

Length of CDS

1632

Coding sequence (CDS) position

1099 / 1101

cDNA position

1157 / 1159

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.31 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:

22:28695868AG>A_8_ENST00000650281

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.40, LOF (oe): 1.07, misssense (oe): 1.00, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000650281.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1100delC
g.46554delC

AA changes

T367Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		367	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	367						D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKITDFG HSKILGETSL MRTLCGTPTY LAPEVLVSVG TAGYNRAVDC WSLGVILFIC
LSGYPPFSEH RTQVSLKDQI TSGKYNFIPE VWAEVSEKAL DLVKKLLVVD PKARFTTEEA
LRHPWLQDED MKRKFQDLLS EENESTALPQ VLAQPSTSRK RPREGEAEGA ETTKRPAVCA
AVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQYLHE NGIIHRDLKP ENVLLSSQEE
DCLIKIMILG TPRFWERPLS *

Position of stopcodon in wt / mu CDS

1632 / 1143

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

544 / 381

Position of stopcodon in wt / mu cDNA

1792 / 1303

Position of start ATG in wt / mu cDNA

161 / 161

Last intron/exon boundary

1702

Theoretical NMD boundary in CDS

1491

Length of CDS

1632

Coding sequence (CDS) position

1099 / 1101

cDNA position

1259 / 1261

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

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:

22:28695868AG>A_9_ENST00000403642

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.68, LOF (oe): 1.25, misssense (oe): 0.98, synonymous (oe): 0.80 ? (gnomAD)

Ensembl transcript ID

ENST00000403642.5

Genbank transcript ID

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.827delC
g.46554delC

AA changes

T276Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		276	S	S	Q	E	E	D	C	L	I	K	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	276	S	S	Q	E	E	D	C	L	I	K	I	M	I	L	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
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
270	279	HELIX		lost
288	302	STRAND		lost
302	308	BINDING	ATP	lost
307	309	STRAND		lost
310	313	HELIX		lost
314	316	HELIX		lost
321	340	HELIX		lost
347	347	ACT_SITE		lost
350	352	HELIX		lost
351	352	BINDING	ATP	lost
353	361	STRAND		lost
364	366	STRAND		lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GGACTGTCTTATAAAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GGACTGTCTTATAAAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLVFVF FDLTVDDQSV
YPKALRDEYI MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE
TEIEILKKLN HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM
LLAVQYLHEN GIIHRDLKPE NVLLSSQEED CLIKITDFGH SKILGETSLM RTLCGTPTYL
APEVLVSVGT AGYNRAVDCW SLGVILFICL SGYPPFSEHR TQVSLKDQIT SGKYNFIPEV
WAEVSEKALD LVKKLLVVDP KARFTTEEAL RHPWLQDEDM KRKFQDLLSE ENESTALPQV
LAQPSTSRKR PREGEAEGAE TTKRPAVCAA VL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLVFVF FDLTVDDQSV
YPKALRDEYI MSKTLGSGAC GEVKLAFERK TCKKVAIKII SKRKFAIGSA READPALNVE
TEIEILKKLN HPCIIKIKNF FDAEDYYIVL ELMEGGELFD KVVGNKRLKE ATCKLYFYQM
LLAVQYLHEN GIIHRDLKPE NVLLSSQEED CLIKIMILGT PRFWERPLS*

Position of stopcodon in wt / mu CDS

1359 / 870

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

453 / 290

Position of stopcodon in wt / mu cDNA

1359 / 870

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

1269

Theoretical NMD boundary in CDS

1218

Length of CDS

1359

Coding sequence (CDS) position

826 / 828

cDNA position

826 / 828

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

Speed

0.41 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:

22:28695868AG>A_10_ENST00000348295

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Frameshift
Heterozygous in gnomAD
Known disease mutation: ClinVar ID 128042 (pathogenic)
NMD
Protein features (might be) affected

Model: complex_aae
Tree vote: 10|0 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr22:28695869delG (GRCh38)

Gene symbol

Gene constraints

LOEUF: 1.40, LOF (oe): 1.07, misssense (oe): 0.99, synonymous (oe): 0.83 ? (gnomAD)

Ensembl transcript ID

ENST00000348295.7

Genbank transcript ID

NM_145862 (by similarity)

UniProt / AlphaMissense peptide

CHK2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.1013delC
g.46554delC

AA changes

T338Mfs*15

Frameshift

Yes

Length of protein

NMD

Pathogenic variant (ClinVar)

Li-Fraumeni syndrome
Li-Fraumeni syndrome 1
Breast cancer, susceptibility to
Carcinoma of pancreas
TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL
Malignant tumor of breast
Bone osteosarcoma
Hereditary breast ovarian cancer syndrome
Leiomyosarcoma
Breast neoplasm
Inflammation of the large intestine
Hematochezia
Colitis
Thrombocytopenia
Breast-ovarian cancer, familial, susceptibility to, 1
Li-Fraumeni syndrome 2
Breast and colorectal cancer, susceptibility to
CHEK2-related disorder
NICE approved PARP inhibitor treatment
CHEK2-related cancer predisposition
Malignant tumor of prostate
Inherited breast cancer and ovarian cancer
Familial cancer of breast
Colorectal cancer
Predisposition to cancer
Ovarian neoplasm
Hereditary cancer-predisposing syndrome
Astrocytoma
Breast and/or ovarian cancer
Breast carcinoma

pathogenic

Variant DBs

dbSNP ID	rs555607708
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	5	3457	3462

Protein conservation

Species	Match	AA	Alignment
Human		338	Y	F	Y	Q	M	L	L	A	V	Q	I	T	D	F	G	H	S	K	I	L	G	E	T	S	L	M	R
mutated	partly conserved	338	Y	F	Y	Q	M	L	L	A	V	Q	I	M	I	L	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
1	543	CHAIN		lost
220	486	DOMAIN	Protein kinase	lost
321	340	HELIX		lost
347	347	ACT_SITE		lost
350	352	HELIX		lost
351	352	BINDING	ATP	lost
353	361	STRAND		lost
364	366	STRAND		lost
368	368	BINDING	ATP	lost
368	394	REGION		lost
369	371	HELIX		lost
379	379	MOD_RES	Phosphoserine	lost
379	385	HELIX		lost
383	383	MOD_RES	Phosphothreonine	lost
387	387	MOD_RES	Phosphothreonine	lost
388	390	HELIX		lost
393	398	HELIX		lost
399	403	TURN		lost
407	422	HELIX		lost
429	431	STRAND		lost
436	442	HELIX		lost
449	452	HELIX		lost
456	456	MOD_RES	Phosphoserine	lost
457	466	HELIX		lost
471	473	TURN		lost
477	481	HELIX		lost
484	486	HELIX		lost
489	502	HELIX		lost
504	506	TURN		lost
506	538	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.709	1
	8.668	1
(flanking)	6.943	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

5

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

22

Strand

-1

Original gDNA sequence snippet

TTGTACTGAATTTTAGATTACTGATTTTGGGCACTCCAAGA

Altered gDNA sequence snippet

TTGTACTGAATTTTAGATTATGATTTTGGGCACTCCAAGA

Original cDNA sequence snippet

GCTCTTGGCTGTGCAGATTACTGATTTTGGGCACTCCAAGA

Altered cDNA sequence snippet

GCTCTTGGCTGTGCAGATTATGATTTTGGGCACTCCAAGA

Wildtype AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQITDF GHSKILGETS LMRTLCGTPT
YLAPEVLVSV GTAGYNRAVD CWSLGVILFI CLSGYPPFSE HRTQVSLKDQ ITSGKYNFIP
EVWAEVSEKA LDLVKKLLVV DPKARFTTEE ALRHPWLQDE DMKRKFQDLL SEENESTALP
QVLAQPSTSR KRPREGEAEG AETTKRPAVC AAVL*

Mutated AA sequence

MSRESDVEAQ QSHGSSACSQ PHGSVTQSQG SSSQSQGISS SSTSTMPNSS QSSHSSSGTL
SSLETVSTQE LYSIPEDQEP EDQEPEEPTP APWARLWALQ DGFANLECVN DNYWFGRDKS
CEYCFDEPLL KRTDKYRTYS KKHFRIFREV GPKNSYIAYI EDHSGNGTFV NTELVGKGKR
RPLNNNSEIA LSLSRNKVFV FFDLTVDDQS VYPKALRDEY IMSKTLGSGA CGEVKLAFER
KTCKKVAIKI ISKRKFAIGS AREADPALNV ETEIEILKKL NHPCIIKIKN FFDAEDYYIV
LELMEGGELF DKVVGNKRLK EATCKLYFYQ MLLAVQIMIL GTPRFWERPL S*

Position of stopcodon in wt / mu CDS

1545 / 1056

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

515 / 352

Position of stopcodon in wt / mu cDNA

1617 / 1128

Position of start ATG in wt / mu cDNA

73 / 73

Last intron/exon boundary

1527

Theoretical NMD boundary in CDS

1404

Length of CDS

1545

Coding sequence (CDS) position

1012 / 1014

cDNA position

1084 / 1086

gDNA position

46553 / 46555

Chromosomal position

28695868 / 28695870

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