MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000566069
Querying Taster for transcript #2: ENST00000261584
Querying Taster for transcript #3: ENST00000568219
Querying Taster for transcript #4: ENST00000697374
Querying Taster for transcript #5: ENST00000713774
Querying Taster for transcript #6: ENST00000697376
Querying Taster for transcript #7: ENST00000697377
Querying Taster for transcript #8: ENST00000697383
Querying Taster for transcript #9: ENST00000697379
Querying Taster for transcript #10: ENST00000561514
MT speed 0.33 s - this script 2.776696 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length
ENST00000566069	PALB2	Deleterious	82\|18	3utr	No	Single base exchange	N/A
ENST00000561514	PALB2	Deleterious	122\|78	without_aae	No	Single base exchange	Normal
ENST00000697376	PALB2	Benign	37\|63	3utr	No	Single base exchange	N/A
ENST00000697374	PALB2	Benign	64\|136	without_aae	No	Single base exchange	Normal
ENST00000713774	PALB2	Benign	64\|136	without_aae	No	Single base exchange	Normal
ENST00000697377	PALB2	Benign	64\|136	without_aae	No	Single base exchange	Normal
ENST00000697383	PALB2	Benign	64\|136	without_aae	No	Single base exchange	Normal
ENST00000697379	PALB2	Benign	64\|136	without_aae	No	Single base exchange	Normal
ENST00000568219	PALB2	Benign	87\|113	without_aae	No	Single base exchange	Normal
ENST00000261584(MANE Select)	PALB2	Benign	94\|106	without_aae	No	Single base exchange	Normal

MutationT@ster 2025

Variant:

16:23603537A>G_1_ENST00000566069

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 82|18 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

LOEUF: 1.54, LOF (oe): 0.62, misssense (oe): 0.90, synonymous (oe): 0.82 ? (gnomAD)

Ensembl transcript ID

ENST00000566069.6

Genbank transcript ID

NM_001407302 (by similarity), NM_001407301 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.3473T>C
g.37785T>C

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	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	1

?

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

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MDEPPGKPLS CEEKEKLKEK LAFLKREYSK TLARLQRAQR AEKIKHSIKK TVEEQDCLSQ
QDLSPQLKHS EPKNKICVYD KLHIKTHLDE ETGEKTSITL DVGPESFNPG DGPGGLPIQR
TDDTQEHFPH RVSDPSGEQK QKLPSRRKKQ QKRTFISQER DCVFGTDSLR LSGKRLKEQE
EISSKNPARS PVTEIRTHLL SLKSELPDSP EPVTEINEDS VLIPPTAQPE KGVDTFLRRP
NFTRATTVPL QTLSDSGSSQ HLEHIPPKGS SELTTHDLKN IRFTSPVSLE AQGKKMTVST
DNLLVNKAIS KSGQLPTSSN LEANISCSLN ELTYNNLPAN ENQNLKEQNQ TEKSLKSPSD
TLDGRNENLQ ESEILSQPKS LSLEATSPLS AEKHSCTVPE GLLFPAEYYV RTTRSMSNCQ
RKVAVEAVIQ SHLDVKKKGF KNKNKDASKN LNLSNEETDQ SEIRMSGTCT GQPSSRTSQK
LLSLTKVSSP AGPTEDNDLS RKAVAQAPGR RYTGKRKSAC TPASDHCEPL LPTSSLSIVN
RSKEEVTSHK YQHEKLFIQV KGKKSRHQKE DSLSWSNSAY LSLDDDAFTA PFHRDGMLSL
KQLLSFLSIT DFQLPDEDFG PLKLEKVKSC SEKPVEPFES KMFGERHLKE GSCIFPEELS
PKRMDTEMED LEEDLIVLPG KSHPKRPNSQ SQHTKTGLSS SILLYTPLNT VAPDDNDRPT
TDMCSPAFPI LGTTPAFGPQ GSYEKASTEV AGRTCCTPQL AHLKDSVCLA SDTKQFDSSG
SPAKPHTTLQ VSGRQGQPTC DCDSVPPGTP PPIESFTFKE NQLCRNTCQE LHKHSVEQTE
TAELPASDSI NPGNLQLVSE LKNPSGSCSV DVSAMFWERA GCKEPCIITA CEDVVSLWKA
LDAWQWEKLY TWHFAEVPVL QIVPVPDVYN LVCVALGNLE IREIRALFCS SDDESEKQVL
LKSGNIKAVL GLTKRRLVSS SGTLSDQQVE VMTFAEDGGG KENQFLMPPE ETILTFAEVQ
GMQEALLGTT IMNNIVIWNL KTGQLLKKMH IDDSYQASVC HKAYSEMVPG R*

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

140 / 140

Last intron/exon boundary

3340

Theoretical NMD boundary in CDS

3150

Length of CDS

3216

Coding sequence (CDS) position

N/A

cDNA position

3473

gDNA position

37785

Chromosomal position

23603537

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

16:23603537A>G_10_ENST00000561514

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 122|78 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

LOEUF: 1.18, LOF (oe): 0.60, misssense (oe): 0.99, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000561514.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3489T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKNPSGSC SVDVSAMFWE RAGCKEPCII TACEDVVSLW
KALDAWQWEK LYTWHFAEVP VLQIVPVPDV YNLVCVALGN LEIREIRALF CSSDDESEKQ
VLLKSGNIKA VLGLTKRRLV SSSGTLSDQQ VEVMTFAEDG GGKENQFLMP PEETILTFAE
VQGMQEALLG TTIMNNIVIW NLKTGQLLKK MHIDDSYQAS VCHKAYSEMG LLFIVLSHPC
AKESESLRSP VFQLIVINPK TTLSVGVMLY CLPPGQAGRF LEGDVKDHCA AAILTSGTIA
IWDLLLGQCT ALLPPVSDQH WSFVKWSGTD SHLLAGQKDG NIFVYHYS*

Mutated AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKNPSGSC SVDVSAMFWE RAGCKEPCII TACEDVVSLW
KALDAWQWEK LYTWHFAEVP VLQIVPVPDV YNLVCVALGN LEIREIRALF CSSDDESEKQ
VLLKSGNIKA VLGLTKRRLV SSSGTLSDQQ VEVMTFAEDG GGKENQFLMP PEETILTFAE
VQGMQEALLG TTIMNNIVIW NLKTGQLLKK MHIDDSYQAS VCHKAYSEMG LLFIVLSHPC
AKESESLRSP VFQLIVINPK TTLSVGVMLY CLPPGQAGRF LEGDVKDHCA AAILTSGTIA
IWDLLLGQCT ALLPPVSDQH WSFVKWSGTD SHLLAGQKDG NIFVYHYS*

Position of stopcodon in wt / mu CDS

3567 / 3567

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

1189 / 1189

Position of stopcodon in wt / mu cDNA

4566 / 4566

Position of start ATG in wt / mu cDNA

1000 / 1000

Last intron/exon boundary

4355

Theoretical NMD boundary in CDS

3305

Length of CDS

3567

Coding sequence (CDS) position

3489

cDNA position

4488

gDNA position

37785

Chromosomal position

23603537

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:

16:23603537A>G_6_ENST00000697376

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 37|63 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000697376.1

Genbank transcript ID

NM_001407313 (by similarity), NM_001407311 (by similarity), NM_001407310 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.3636T>C
g.37785T>C

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	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	1

?

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

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MTVSTDNLLV NKAISKSGQL PTSSNLEANI SCSLNELTYN NLPANENQNL KEQNQTEKSL
KSPSDTLDGR NENLQESEIL SQPKSLSLEA TSPLSAEKHS CTVPEGLLFP AEYYVRTTRS
MSNCQRKVAV EAVIQSHLDV KKKGFKNKNK DASKNLNLSN EETDQSEIRM SGTCTGQPSS
RTSQKLLSLT KVSSPAGPTE DNDLSRKAVA QAPGRRYTGK RKSACTPASD HCEPLLPTSS
LSIVNRSKEE VTSHKYQHEK LFIQVKGKKS RHQKEDSLSW SNSAYLSLDD DAFTAPFHRD
GMLSLKQLLS FLSITDFQLP DEDFGPLKLE KVKSCSEKPV EPFESKMFGE RHLKEGSCIF
PEELSPKRMD TEMEDLEEDL IVLPGKSHPK RPNSQSQHTK TGLSSSILLY TPLNTVAPDD
NDRPTTDMCS PAFPILGTTP AFGPQGSYEK ASTEVAGRTC CTPQLAHLKD SVCLASDTKQ
FDSSGSPAKP HTTLQVSGRQ GQPTCDCDSV PPGTPPPIES FTFKENQLCR NTCQELHKHS
VEQTETAELP ASDSINPGNL QLVSELKNPS GSCSVDVSAM FWERAGCKEP CIITACEDVV
SLWKALDAWQ WEKLYTWHFA EVPVLQIVPV PDVYNLVCVA LGNLEIREIR ALFCSSDDES
EKQVLLKSGN IKAVLGLTKR RLVSSSGTLS DQQVEVMTFA EDGGGKENQF LMPPEETILT
FAEVQGMQEA LLGTTIMNNI VIWNLKTGQL LKKMHIDDSY QASVCHKAYS EMVPGR*

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

1188 / 1188

Last intron/exon boundary

3503

Theoretical NMD boundary in CDS

2265

Length of CDS

2331

Coding sequence (CDS) position

N/A

cDNA position

3636

gDNA position

37785

Chromosomal position

23603537

Speed

0.09 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:

16:23603537A>G_4_ENST00000697374

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 64|136 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000697374.1

Genbank transcript ID

NM_001407304 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2598T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MTVSTDNLLV NKAISKSGQL PTSSNLEANI SCSLNELTYN NLPANENQNL KEQNQTEKSL
KSPSDTLDGR NENLQESEIL SQPKSLSLEA TSPLSAEKHS CTVPEGLLFP AEYYVRTTRS
MSNCQRKVAV EAVIQSHLDV KKKGFKNKNK DASKNLNLSN EETDQSEIRM SGTCTGQPSS
RTSQKLLSLT KVSSPAGPTE DNDLSRKAVA QAPGRRYTGK RKSACTPASD HCEPLLPTSS
LSIVNRSKEE VTSHKYQHEK LFIQVKGKKS RHQKEDSLSW SNSAYLSLDD DAFTAPFHRD
GMLSLKQLLS FLSITDFQLP DEDFGPLKLE KVKSCSEKPV EPFESKMFGE RHLKEGSCIF
PEELSPKRMD TEMEDLEEDL IVLPGKSHPK RPNSQSQHTK TGLSSSILLY TPLNTVAPDD
NDRPTTDMCS PAFPILGTTP AFGPQGSYEK ASTEVAGRTC CTPQLAHLKD SVCLASDTKQ
FDSSGSPAKP HTTLQVSGRQ GQPTCDCDSV PPGTPPPIES FTFKENQLCR NTCQELHKHS
VEQTETAELP ASDSINPGNL QLVSELKNPS GSCSVDVSAM FWERAGCKEP CIITACEDVV
SLWKALDAWQ WEKLYTWHFA EVPVLQIVPV PDVYNLVCVA LGNLEIREIR ALFCSSDDES
EKQVLLKSGN IKAVLGLTKR RLVSSSGTLS DQQVEVMTFA EDGGGKENQF LMPPEETILT
FAEVQGMQEA LLGTTIMNNI VIWNLKTGQL LKKMHIDDSY QASVCHKAYS EMGLLFIVLS
HPCAKESESL RSPVFQLIVI NPKTTLSVGV MLYCLPPGQA GRFLEGDVKD HCAAAILTSG
TIAIWDLLLG QCTALLPPVS DQHWSFVKWS GTDSHLLAGQ KDGNIFVYHY S*

Mutated AA sequence

MTVSTDNLLV NKAISKSGQL PTSSNLEANI SCSLNELTYN NLPANENQNL KEQNQTEKSL
KSPSDTLDGR NENLQESEIL SQPKSLSLEA TSPLSAEKHS CTVPEGLLFP AEYYVRTTRS
MSNCQRKVAV EAVIQSHLDV KKKGFKNKNK DASKNLNLSN EETDQSEIRM SGTCTGQPSS
RTSQKLLSLT KVSSPAGPTE DNDLSRKAVA QAPGRRYTGK RKSACTPASD HCEPLLPTSS
LSIVNRSKEE VTSHKYQHEK LFIQVKGKKS RHQKEDSLSW SNSAYLSLDD DAFTAPFHRD
GMLSLKQLLS FLSITDFQLP DEDFGPLKLE KVKSCSEKPV EPFESKMFGE RHLKEGSCIF
PEELSPKRMD TEMEDLEEDL IVLPGKSHPK RPNSQSQHTK TGLSSSILLY TPLNTVAPDD
NDRPTTDMCS PAFPILGTTP AFGPQGSYEK ASTEVAGRTC CTPQLAHLKD SVCLASDTKQ
FDSSGSPAKP HTTLQVSGRQ GQPTCDCDSV PPGTPPPIES FTFKENQLCR NTCQELHKHS
VEQTETAELP ASDSINPGNL QLVSELKNPS GSCSVDVSAM FWERAGCKEP CIITACEDVV
SLWKALDAWQ WEKLYTWHFA EVPVLQIVPV PDVYNLVCVA LGNLEIREIR ALFCSSDDES
EKQVLLKSGN IKAVLGLTKR RLVSSSGTLS DQQVEVMTFA EDGGGKENQF LMPPEETILT
FAEVQGMQEA LLGTTIMNNI VIWNLKTGQL LKKMHIDDSY QASVCHKAYS EMGLLFIVLS
HPCAKESESL RSPVFQLIVI NPKTTLSVGV MLYCLPPGQA GRFLEGDVKD HCAAAILTSG
TIAIWDLLLG QCTALLPPVS DQHWSFVKWS GTDSHLLAGQ KDGNIFVYHY S*

Position of stopcodon in wt / mu CDS

2676 / 2676

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

892 / 892

Position of stopcodon in wt / mu cDNA

4084 / 4084

Position of start ATG in wt / mu cDNA

1409 / 1409

Last intron/exon boundary

3873

Theoretical NMD boundary in CDS

2414

Length of CDS

2676

Coding sequence (CDS) position

2598

cDNA position

4006

gDNA position

37785

Chromosomal position

23603537

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:

16:23603537A>G_5_ENST00000713774

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 64|136 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000713774.1

Genbank transcript ID

NM_001407299 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3246T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MDEPPGKPLS CEEKEKLKEK LAFLKREYSK TLARLQRAQR AEKIKHSIKK TVEEQDCLSQ
QDLSPQLKHS EPKNKICVYD KLHIKTHLDE ETGEKTSITL DVGPESFNPG DGPGGLPIQR
TDDTQEHFPH RVSDPSGEQK QKLPSRRKKQ QKRTFISQER DCVFGTDSLR LSGKRLKEQE
EISSKNPARS PVTEIRTHLL SLKSELPDSP EPVTEINEDS VLIPPTAQPE KGVDTFLRRP
NFTRATTVPL QTLSDSGSSQ HLEHIPPKGS SELTTHDLKN IRFTSPVSLE AQGKKMTVST
DNLLVNKAIS KSGQLPTSSN LEANISCSLN ELTYNNLPAN ENQNLKEQNQ TEKSLKSPSD
TLDGRNENLQ ESEILSQPKS LSLEATSPLS AEKHSCTVPE GLLFPAEYYV RTTRSMSNCQ
RKVAVEAVIQ SHLDVKKKGF KNKNKDASKN LNLSNEETDQ SEIRMSGTCT GQPSSRTSQK
LLSLTKVSSP AGPTEDNDLS RKAVAQAPGR RYTGKRKSAC TPASDHCEPL LPTSSLSIVN
RSKEEVTSHK YQHEKLFIQV KGKKSRHQKE DSLSWSNSAY LSLDDDAFTA PFHRDGMLSL
KQLLSFLSIT DFQLPDEDFG PLKLEKVKSC SEKPVEPFES KMFGERHLKE GSCIFPEELS
PKRMDTEMED LEEDLIVLPG KSHPKRPNSQ SQHTKTGLSS SILLYTPLNT VAPDDNDRPT
TDMCSPAFPI LGTTPAFGPQ GSYEKASTEV AGRTCCTPQL AHLKDSVCLA SDTKQFDSSG
SPAKPHTTLQ VSGRQGQPTC DCDSVPPGTP PPIESFTFKE NQLCRNTCQE LHKHSVEQTE
TAELPASDSI NPGNLQLVSE LKNPSGSCSV DVSAMFWERA GCKEPCIITA CEDVVSLWKA
LDAWQWEKLY TWHFAEVPVL QIVPVPDVYN LVCVALGNLE IREIRALFCS SDDESEKQVL
LKSGNIKAVL GLTKRRLVSS SGTLSDQQVE VMTFAEDGGG KENQFLMPPE ETILTFAEVQ
GMQEALLGTT IMNNIVIWFL EGDVKDHCAA AILTSGTIAI WDLLLGQCTA LLPPVSDQHW
SFVKWSGTDS HLLAGQKDGN IFVYHYS*

Mutated AA sequence

MDEPPGKPLS CEEKEKLKEK LAFLKREYSK TLARLQRAQR AEKIKHSIKK TVEEQDCLSQ
QDLSPQLKHS EPKNKICVYD KLHIKTHLDE ETGEKTSITL DVGPESFNPG DGPGGLPIQR
TDDTQEHFPH RVSDPSGEQK QKLPSRRKKQ QKRTFISQER DCVFGTDSLR LSGKRLKEQE
EISSKNPARS PVTEIRTHLL SLKSELPDSP EPVTEINEDS VLIPPTAQPE KGVDTFLRRP
NFTRATTVPL QTLSDSGSSQ HLEHIPPKGS SELTTHDLKN IRFTSPVSLE AQGKKMTVST
DNLLVNKAIS KSGQLPTSSN LEANISCSLN ELTYNNLPAN ENQNLKEQNQ TEKSLKSPSD
TLDGRNENLQ ESEILSQPKS LSLEATSPLS AEKHSCTVPE GLLFPAEYYV RTTRSMSNCQ
RKVAVEAVIQ SHLDVKKKGF KNKNKDASKN LNLSNEETDQ SEIRMSGTCT GQPSSRTSQK
LLSLTKVSSP AGPTEDNDLS RKAVAQAPGR RYTGKRKSAC TPASDHCEPL LPTSSLSIVN
RSKEEVTSHK YQHEKLFIQV KGKKSRHQKE DSLSWSNSAY LSLDDDAFTA PFHRDGMLSL
KQLLSFLSIT DFQLPDEDFG PLKLEKVKSC SEKPVEPFES KMFGERHLKE GSCIFPEELS
PKRMDTEMED LEEDLIVLPG KSHPKRPNSQ SQHTKTGLSS SILLYTPLNT VAPDDNDRPT
TDMCSPAFPI LGTTPAFGPQ GSYEKASTEV AGRTCCTPQL AHLKDSVCLA SDTKQFDSSG
SPAKPHTTLQ VSGRQGQPTC DCDSVPPGTP PPIESFTFKE NQLCRNTCQE LHKHSVEQTE
TAELPASDSI NPGNLQLVSE LKNPSGSCSV DVSAMFWERA GCKEPCIITA CEDVVSLWKA
LDAWQWEKLY TWHFAEVPVL QIVPVPDVYN LVCVALGNLE IREIRALFCS SDDESEKQVL
LKSGNIKAVL GLTKRRLVSS SGTLSDQQVE VMTFAEDGGG KENQFLMPPE ETILTFAEVQ
GMQEALLGTT IMNNIVIWFL EGDVKDHCAA AILTSGTIAI WDLLLGQCTA LLPPVSDQHW
SFVKWSGTDS HLLAGQKDGN IFVYHYS*

Position of stopcodon in wt / mu CDS

3324 / 3324

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

1108 / 1108

Position of stopcodon in wt / mu cDNA

3478 / 3478

Position of start ATG in wt / mu cDNA

155 / 155

Last intron/exon boundary

3267

Theoretical NMD boundary in CDS

3062

Length of CDS

3324

Coding sequence (CDS) position

3246

cDNA position

3400

gDNA position

37785

Chromosomal position

23603537

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:

16:23603537A>G_7_ENST00000697377

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 64|136 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000697377.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3327T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKVPVLQI VPVPDVYNLV CVALGNLEIR EIRALFCSSD
DESEKQVLLK SGNIKAVLGL TKRRLVSSSG TLSDQQVEVM TFAEDGGGKE NQFLMPPEET
ILTFAEVQGM QEALLGTTIM NNIVIWNLKT GQLLKKMHID DSYQASVCHK AYSEMGLLFI
VLSHPCAKES ESLRSPVFQL IVINPKTTLS VGVMLYCLPP GQAGRFLEGD VKDHCAAAIL
TSGTIAIWDL LLGQCTALLP PVSDQHWSFV KWSGTDSHLL AGQKDGNIFV YHYS*

Mutated AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKVPVLQI VPVPDVYNLV CVALGNLEIR EIRALFCSSD
DESEKQVLLK SGNIKAVLGL TKRRLVSSSG TLSDQQVEVM TFAEDGGGKE NQFLMPPEET
ILTFAEVQGM QEALLGTTIM NNIVIWNLKT GQLLKKMHID DSYQASVCHK AYSEMGLLFI
VLSHPCAKES ESLRSPVFQL IVINPKTTLS VGVMLYCLPP GQAGRFLEGD VKDHCAAAIL
TSGTIAIWDL LLGQCTALLP PVSDQHWSFV KWSGTDSHLL AGQKDGNIFV YHYS*

Position of stopcodon in wt / mu CDS

3405 / 3405

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

1135 / 1135

Position of stopcodon in wt / mu cDNA

3798 / 3798

Position of start ATG in wt / mu cDNA

394 / 394

Last intron/exon boundary

3587

Theoretical NMD boundary in CDS

3143

Length of CDS

3405

Coding sequence (CDS) position

3327

cDNA position

3720

gDNA position

37785

Chromosomal position

23603537

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:

16:23603537A>G_8_ENST00000697383

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 64|136 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000697383.1

Genbank transcript ID

NM_001407314 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1017T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MDEPPGKPLS CEEKEKTETA ELPASDSINP GNLQLVSELK NPSGSCSVDV SAMFWERAGC
KEPCIITACE DVVSLWKALD AWQWEKLYTW HFAEVPVLQI VPVPDVYNLV CVALGNLEIR
EIRALFCSSD DESEKQVLLK SGNIKAVLGL TKRRLVSSSG TLSDQQVEVM TFAEDGGGKE
NQFLMPPEET ILTFAEVQGM QEALLGTTIM NNIVIWNLKT GQLLKKMHID DSYQASVCHK
AYSEMGLLFI VLSHPCAKES ESLRSPVFQL IVINPKTTLS VGVMLYCLPP GQAGRFLEGD
VKDHCAAAIL TSGTIAIWDL LLGQCTALLP PVSDQHWSFV KWSGTDSHLL AGQKDGNIFV
YHYS*

Mutated AA sequence

MDEPPGKPLS CEEKEKTETA ELPASDSINP GNLQLVSELK NPSGSCSVDV SAMFWERAGC
KEPCIITACE DVVSLWKALD AWQWEKLYTW HFAEVPVLQI VPVPDVYNLV CVALGNLEIR
EIRALFCSSD DESEKQVLLK SGNIKAVLGL TKRRLVSSSG TLSDQQVEVM TFAEDGGGKE
NQFLMPPEET ILTFAEVQGM QEALLGTTIM NNIVIWNLKT GQLLKKMHID DSYQASVCHK
AYSEMGLLFI VLSHPCAKES ESLRSPVFQL IVINPKTTLS VGVMLYCLPP GQAGRFLEGD
VKDHCAAAIL TSGTIAIWDL LLGQCTALLP PVSDQHWSFV KWSGTDSHLL AGQKDGNIFV
YHYS*

Position of stopcodon in wt / mu CDS

1095 / 1095

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

365 / 365

Position of stopcodon in wt / mu cDNA

1259 / 1259

Position of start ATG in wt / mu cDNA

165 / 165

Last intron/exon boundary

1048

Theoretical NMD boundary in CDS

833

Length of CDS

1095

Coding sequence (CDS) position

1017

cDNA position

1181

gDNA position

37785

Chromosomal position

23603537

Speed

0.01 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:

16:23603537A>G_9_ENST00000697379

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 64|136 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

no data

Ensembl transcript ID

ENST00000697379.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3489T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKNPSGSC SVDVSAMFWE RAGCKEPCII TACEDVVSLW
KALDAWQWEK LYTWHFAEVP VLQIVPVPDV YNLVCVALGN LEIREIRALF CSSDDESEKQ
VLLKSGNIKA VLGLTKRRLV SSSGTLSDQQ VEVMTFAEDG GGKENQFLMP PEETILTFAE
VQGMQEALLG TTIMNNIVIW NLKTGQLLKK MHIDDSYQAS VCHKAYSEMG LLFIVLSHPC
AKESESLRSP VFQLIVINPK TTLSVGVMLY CLPPGQAGRF LEGDVKDHCA AAILTSGTIA
IWDLLLGQCT ALLPPVSDQH WSFVKWSGTD SHLLAGQKDG NIFVYHYS*

Mutated AA sequence

MFPACADVIL ILAYLLVELK EKLAFLKREY SKTLARLQRA QRAEKIKHSI KKTVEEQDCL
SQQDLSPQLK HSEPKNKICV YDKLHIKTHL DEETGEKTSI TLDVGPESFN PGDGPGGLPI
QRTDDTQEHF PHRVSDPSGE QKQKLPSRRK KQQKRTFISQ ERDCVFGTDS LRLSGKRLKE
QEEISSKNPA RSPVTEIRTH LLSLKSELPD SPEPVTEINE DSVLIPPTAQ PEKGVDTFLR
RPNFTRATTV PLQTLSDSGS SQHLEHIPPK GSSELTTHDL KNIRFTSPVS LEAQGKKMTV
STDNLLVNKA ISKSGQLPTS SNLEANISCS LNELTYNNLP ANENQNLKEQ NQTEKSLKSP
SDTLDGRNEN LQESEILSQP KSLSLEATSP LSAEKHSCTV PEGLLFPAEY YVRTTRSMSN
CQRKVAVEAV IQSHLDVKKK GFKNKNKDAS KNLNLSNEET DQSEIRMSGT CTGQPSSRTS
QKLLSLTKVS SPAGPTEDND LSRKAVAQAP GRRYTGKRKS ACTPASDHCE PLLPTSSLSI
VNRSKEEVTS HKYQHEKLFI QVKGKKSRHQ KEDSLSWSNS AYLSLDDDAF TAPFHRDGML
SLKQLLSFLS ITDFQLPDED FGPLKLEKVK SCSEKPVEPF ESKMFGERHL KEGSCIFPEE
LSPKRMDTEM EDLEEDLIVL PGKSHPKRPN SQSQHTKTGL SSSILLYTPL NTVAPDDNDR
PTTDMCSPAF PILGTTPAFG PQGSYEKAST EVAGRTCCTP QLAHLKDSVC LASDTKQFDS
SGSPAKPHTT LQVSGRQGQP TCDCDSVPPG TPPPIESFTF KENQLCRNTC QELHKHSVEQ
TETAELPASD SINPGNLQLV SELKNPSGSC SVDVSAMFWE RAGCKEPCII TACEDVVSLW
KALDAWQWEK LYTWHFAEVP VLQIVPVPDV YNLVCVALGN LEIREIRALF CSSDDESEKQ
VLLKSGNIKA VLGLTKRRLV SSSGTLSDQQ VEVMTFAEDG GGKENQFLMP PEETILTFAE
VQGMQEALLG TTIMNNIVIW NLKTGQLLKK MHIDDSYQAS VCHKAYSEMG LLFIVLSHPC
AKESESLRSP VFQLIVINPK TTLSVGVMLY CLPPGQAGRF LEGDVKDHCA AAILTSGTIA
IWDLLLGQCT ALLPPVSDQH WSFVKWSGTD SHLLAGQKDG NIFVYHYS*

Position of stopcodon in wt / mu CDS

3567 / 3567

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

1189 / 1189

Position of stopcodon in wt / mu cDNA

3866 / 3866

Position of start ATG in wt / mu cDNA

300 / 300

Last intron/exon boundary

3655

Theoretical NMD boundary in CDS

3305

Length of CDS

3567

Coding sequence (CDS) position

3489

cDNA position

3788

gDNA position

37785

Chromosomal position

23603537

Speed

0.01 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:

16:23603537A>G_3_ENST00000568219

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 87|113 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

LOEUF: 1.00, LOF (oe): 0.81, misssense (oe): 0.95, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000568219.5

Genbank transcript ID

NM_001407308 (by similarity), NM_001407306 (by similarity), NM_001407312 (by similarity), NM_001407307 (by similarity), NM_001407309 (by similarity), NM_001407305 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.2598T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MTVSTDNLLV NKAISKSGQL PTSSNLEANI SCSLNELTYN NLPANENQNL KEQNQTEKSL
KSPSDTLDGR NENLQESEIL SQPKSLSLEA TSPLSAEKHS CTVPEGLLFP AEYYVRTTRS
MSNCQRKVAV EAVIQSHLDV KKKGFKNKNK DASKNLNLSN EETDQSEIRM SGTCTGQPSS
RTSQKLLSLT KVSSPAGPTE DNDLSRKAVA QAPGRRYTGK RKSACTPASD HCEPLLPTSS
LSIVNRSKEE VTSHKYQHEK LFIQVKGKKS RHQKEDSLSW SNSAYLSLDD DAFTAPFHRD
GMLSLKQLLS FLSITDFQLP DEDFGPLKLE KVKSCSEKPV EPFESKMFGE RHLKEGSCIF
PEELSPKRMD TEMEDLEEDL IVLPGKSHPK RPNSQSQHTK TGLSSSILLY TPLNTVAPDD
NDRPTTDMCS PAFPILGTTP AFGPQGSYEK ASTEVAGRTC CTPQLAHLKD SVCLASDTKQ
FDSSGSPAKP HTTLQVSGRQ GQPTCDCDSV PPGTPPPIES FTFKENQLCR NTCQELHKHS
VEQTETAELP ASDSINPGNL QLVSELKNPS GSCSVDVSAM FWERAGCKEP CIITACEDVV
SLWKALDAWQ WEKLYTWHFA EVPVLQIVPV PDVYNLVCVA LGNLEIREIR ALFCSSDDES
EKQVLLKSGN IKAVLGLTKR RLVSSSGTLS DQQVEVMTFA EDGGGKENQF LMPPEETILT
FAEVQGMQEA LLGTTIMNNI VIWNLKTGQL LKKMHIDDSY QASVCHKAYS EMGLLFIVLS
HPCAKESESL RSPVFQLIVI NPKTTLSVGV MLYCLPPGQA GRFLEGDVKD HCAAAILTSG
TIAIWDLLLG QCTALLPPVS DQHWSFVKWS GTDSHLLAGQ KDGNIFVYHY S*

Mutated AA sequence

MTVSTDNLLV NKAISKSGQL PTSSNLEANI SCSLNELTYN NLPANENQNL KEQNQTEKSL
KSPSDTLDGR NENLQESEIL SQPKSLSLEA TSPLSAEKHS CTVPEGLLFP AEYYVRTTRS
MSNCQRKVAV EAVIQSHLDV KKKGFKNKNK DASKNLNLSN EETDQSEIRM SGTCTGQPSS
RTSQKLLSLT KVSSPAGPTE DNDLSRKAVA QAPGRRYTGK RKSACTPASD HCEPLLPTSS
LSIVNRSKEE VTSHKYQHEK LFIQVKGKKS RHQKEDSLSW SNSAYLSLDD DAFTAPFHRD
GMLSLKQLLS FLSITDFQLP DEDFGPLKLE KVKSCSEKPV EPFESKMFGE RHLKEGSCIF
PEELSPKRMD TEMEDLEEDL IVLPGKSHPK RPNSQSQHTK TGLSSSILLY TPLNTVAPDD
NDRPTTDMCS PAFPILGTTP AFGPQGSYEK ASTEVAGRTC CTPQLAHLKD SVCLASDTKQ
FDSSGSPAKP HTTLQVSGRQ GQPTCDCDSV PPGTPPPIES FTFKENQLCR NTCQELHKHS
VEQTETAELP ASDSINPGNL QLVSELKNPS GSCSVDVSAM FWERAGCKEP CIITACEDVV
SLWKALDAWQ WEKLYTWHFA EVPVLQIVPV PDVYNLVCVA LGNLEIREIR ALFCSSDDES
EKQVLLKSGN IKAVLGLTKR RLVSSSGTLS DQQVEVMTFA EDGGGKENQF LMPPEETILT
FAEVQGMQEA LLGTTIMNNI VIWNLKTGQL LKKMHIDDSY QASVCHKAYS EMGLLFIVLS
HPCAKESESL RSPVFQLIVI NPKTTLSVGV MLYCLPPGQA GRFLEGDVKD HCAAAILTSG
TIAIWDLLLG QCTALLPPVS DQHWSFVKWS GTDSHLLAGQ KDGNIFVYHY S*

Position of stopcodon in wt / mu CDS

2676 / 2676

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

892 / 892

Position of stopcodon in wt / mu cDNA

3672 / 3672

Position of start ATG in wt / mu cDNA

997 / 997

Last intron/exon boundary

3461

Theoretical NMD boundary in CDS

2414

Length of CDS

2676

Coding sequence (CDS) position

2598

cDNA position

3594

gDNA position

37785

Chromosomal position

23603537

Speed

0.01 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:

16:23603537A>G_2_ENST00000261584

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 94|106 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr16:23603537A>G (GRCh38)

Gene symbol

PALB2

Gene constraints

LOEUF: 0.90, LOF (oe): 0.74, misssense (oe): 0.94, synonymous (oe): 0.93 ? (gnomAD)

Ensembl transcript ID

ENST00000261584.9

Genbank transcript ID

NM_024675 (exact from MANE), NM_001407296 (by similarity), NM_001407297 (by similarity), NM_001407298 (by similarity), NM_001407300 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3483T>C
g.37785T>C

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs372686500
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	42	42

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.918	0.999
	-0.055	0.951
(flanking)	5.805	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

No

Chromosome

16

Strand

-1

Original gDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered gDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Original cDNA sequence snippet

TCTGACCAACATTGGTCTTTTGTGAAATGGTCGGGTACAGA

Altered cDNA sequence snippet

TCTGACCAACATTGGTCTTTCGTGAAATGGTCGGGTACAGA

Wildtype AA sequence

MDEPPGKPLS CEEKEKLKEK LAFLKREYSK TLARLQRAQR AEKIKHSIKK TVEEQDCLSQ
QDLSPQLKHS EPKNKICVYD KLHIKTHLDE ETGEKTSITL DVGPESFNPG DGPGGLPIQR
TDDTQEHFPH RVSDPSGEQK QKLPSRRKKQ QKRTFISQER DCVFGTDSLR LSGKRLKEQE
EISSKNPARS PVTEIRTHLL SLKSELPDSP EPVTEINEDS VLIPPTAQPE KGVDTFLRRP
NFTRATTVPL QTLSDSGSSQ HLEHIPPKGS SELTTHDLKN IRFTSPVSLE AQGKKMTVST
DNLLVNKAIS KSGQLPTSSN LEANISCSLN ELTYNNLPAN ENQNLKEQNQ TEKSLKSPSD
TLDGRNENLQ ESEILSQPKS LSLEATSPLS AEKHSCTVPE GLLFPAEYYV RTTRSMSNCQ
RKVAVEAVIQ SHLDVKKKGF KNKNKDASKN LNLSNEETDQ SEIRMSGTCT GQPSSRTSQK
LLSLTKVSSP AGPTEDNDLS RKAVAQAPGR RYTGKRKSAC TPASDHCEPL LPTSSLSIVN
RSKEEVTSHK YQHEKLFIQV KGKKSRHQKE DSLSWSNSAY LSLDDDAFTA PFHRDGMLSL
KQLLSFLSIT DFQLPDEDFG PLKLEKVKSC SEKPVEPFES KMFGERHLKE GSCIFPEELS
PKRMDTEMED LEEDLIVLPG KSHPKRPNSQ SQHTKTGLSS SILLYTPLNT VAPDDNDRPT
TDMCSPAFPI LGTTPAFGPQ GSYEKASTEV AGRTCCTPQL AHLKDSVCLA SDTKQFDSSG
SPAKPHTTLQ VSGRQGQPTC DCDSVPPGTP PPIESFTFKE NQLCRNTCQE LHKHSVEQTE
TAELPASDSI NPGNLQLVSE LKNPSGSCSV DVSAMFWERA GCKEPCIITA CEDVVSLWKA
LDAWQWEKLY TWHFAEVPVL QIVPVPDVYN LVCVALGNLE IREIRALFCS SDDESEKQVL
LKSGNIKAVL GLTKRRLVSS SGTLSDQQVE VMTFAEDGGG KENQFLMPPE ETILTFAEVQ
GMQEALLGTT IMNNIVIWNL KTGQLLKKMH IDDSYQASVC HKAYSEMGLL FIVLSHPCAK
ESESLRSPVF QLIVINPKTT LSVGVMLYCL PPGQAGRFLE GDVKDHCAAA ILTSGTIAIW
DLLLGQCTAL LPPVSDQHWS FVKWSGTDSH LLAGQKDGNI FVYHYS*

Mutated AA sequence

MDEPPGKPLS CEEKEKLKEK LAFLKREYSK TLARLQRAQR AEKIKHSIKK TVEEQDCLSQ
QDLSPQLKHS EPKNKICVYD KLHIKTHLDE ETGEKTSITL DVGPESFNPG DGPGGLPIQR
TDDTQEHFPH RVSDPSGEQK QKLPSRRKKQ QKRTFISQER DCVFGTDSLR LSGKRLKEQE
EISSKNPARS PVTEIRTHLL SLKSELPDSP EPVTEINEDS VLIPPTAQPE KGVDTFLRRP
NFTRATTVPL QTLSDSGSSQ HLEHIPPKGS SELTTHDLKN IRFTSPVSLE AQGKKMTVST
DNLLVNKAIS KSGQLPTSSN LEANISCSLN ELTYNNLPAN ENQNLKEQNQ TEKSLKSPSD
TLDGRNENLQ ESEILSQPKS LSLEATSPLS AEKHSCTVPE GLLFPAEYYV RTTRSMSNCQ
RKVAVEAVIQ SHLDVKKKGF KNKNKDASKN LNLSNEETDQ SEIRMSGTCT GQPSSRTSQK
LLSLTKVSSP AGPTEDNDLS RKAVAQAPGR RYTGKRKSAC TPASDHCEPL LPTSSLSIVN
RSKEEVTSHK YQHEKLFIQV KGKKSRHQKE DSLSWSNSAY LSLDDDAFTA PFHRDGMLSL
KQLLSFLSIT DFQLPDEDFG PLKLEKVKSC SEKPVEPFES KMFGERHLKE GSCIFPEELS
PKRMDTEMED LEEDLIVLPG KSHPKRPNSQ SQHTKTGLSS SILLYTPLNT VAPDDNDRPT
TDMCSPAFPI LGTTPAFGPQ GSYEKASTEV AGRTCCTPQL AHLKDSVCLA SDTKQFDSSG
SPAKPHTTLQ VSGRQGQPTC DCDSVPPGTP PPIESFTFKE NQLCRNTCQE LHKHSVEQTE
TAELPASDSI NPGNLQLVSE LKNPSGSCSV DVSAMFWERA GCKEPCIITA CEDVVSLWKA
LDAWQWEKLY TWHFAEVPVL QIVPVPDVYN LVCVALGNLE IREIRALFCS SDDESEKQVL
LKSGNIKAVL GLTKRRLVSS SGTLSDQQVE VMTFAEDGGG KENQFLMPPE ETILTFAEVQ
GMQEALLGTT IMNNIVIWNL KTGQLLKKMH IDDSYQASVC HKAYSEMGLL FIVLSHPCAK
ESESLRSPVF QLIVINPKTT LSVGVMLYCL PPGQAGRFLE GDVKDHCAAA ILTSGTIAIW
DLLLGQCTAL LPPVSDQHWS FVKWSGTDSH LLAGQKDGNI FVYHYS*

Position of stopcodon in wt / mu CDS

3561 / 3561

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

1187 / 1187

Position of stopcodon in wt / mu cDNA

3714 / 3714

Position of start ATG in wt / mu cDNA

154 / 154

Last intron/exon boundary

3503

Theoretical NMD boundary in CDS

3299

Length of CDS

3561

Coding sequence (CDS) position

3483

cDNA position

3636

gDNA position

37785

Chromosomal position

23603537

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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