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: ENST00000504120
Querying Taster for transcript #2: ENST00000394633
Querying Taster for transcript #3: ENST00000526136
Querying Taster for transcript #4: ENST00000522353
Querying Taster for transcript #5: ENST00000529859
Querying Taster for transcript #6: ENST00000529619
Querying Taster for transcript #7: ENST00000529310
Querying Taster for transcript #8: ENST00000527624
Querying Taster for transcript #9: ENST00000525929
Querying Taster for transcript #10: ENST00000531613
Querying Taster for transcript #11: ENST00000532602
Querying Taster for transcript #12: ENST00000307360
Querying Taster for transcript #13: ENST00000506939
Querying Taster for transcript #14: ENST00000398640
Querying Taster for transcript #15: ENST00000398631
Querying Taster for transcript #16: ENST00000530339
Querying Taster for transcript #17: ENST00000512229
MT speed 0.22 s - this script 2.795022 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000506939	PCDHA10	Benign	43\|157	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000394633	PCDHA1	Benign	49\|151	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000307360(MANE Select)	PCDHA10	Benign	49\|151	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000530339(MANE Select)	PCDHA4	Benign	49\|151	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000504120(MANE Select)	PCDHA1	Benign	50\|150	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000512229	PCDHA4	Benign	51\|149	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000525929(MANE Select)	PCDHA7	Benign	52\|148	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000398631(MANE Select)	PCDHA12	Benign	53\|147	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000522353(MANE Select)	PCDHA3	Benign	54\|146	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000527624	PCDHA6	Benign	54\|146	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000531613(MANE Select)	PCDHA8	Benign	54\|146	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000529859(MANE Select)	PCDHA5	Benign	55\|145	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000526136(MANE Select)	PCDHA2	Benign	56\|144	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000398640(MANE Select)	PCDHA11	Benign	57\|143	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000529619	PCDHA5	Benign	66\|134	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000529310(MANE Select)	PCDHA6	Benign	73\|127	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD
ENST00000532602(MANE Select)	PCDHA9	Benign	82\|118	without_aae	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

5:140882092A>C_13_ENST00000506939

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 43|157 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA10

Gene constraints

LOEUF: 0.91, LOF (oe): 0.68, misssense (oe): 0.95, synonymous (oe): 1.00 ? (gnomAD)

Ensembl transcript ID

ENST00000506939.6

Genbank transcript ID

NM_031860 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1599+24445A>C
g.26210A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVSRCSCLGV QCLLLSLLLL AAWEVGSGQL HYSVYEEARH GTFVGRIAQD LGLELAELVQ
RLFRVASKRH GDLLEVNLQN GILFVNSRID REELCGRSVE CSIHLEVIVD RPLQVFHVDV
EVKDINDNPP RFSVTEQKLS IPESRLLDSR FPLEGASDAD VGENALLTYK LSPNEYFVLD
IINKKDKDKF PVLVLRKLLD REENPQLKLL LTATDGGKPE FTGSVSLLIL VLDANDNAPI
FDRPVYEVKM YENQVNQTLV IRLNASDSDE GINKEMMYSF SSLVPPTIRR KFWINERTGE
IKVNDAIDFE DSNTYEIHVD VTDKGNPPMV GHCTVLVELL DENDNSPEVI VTSLSLPVKE
DAQVGTVIAL ISVSDHDSGA NGQVTCSLTP HVPFKLVSTY KNYYSLVLDS ALDRERVSAY
ELVVTARDGG SPPLWATASV SVEVADVNDN APAFAQSEYT VFVKENNPPG CHIFTVSAWD
ADAQENALVS YSLVERRLGE RSLSSYVSVH AESGKVYALQ PLDHEELELL QFQPRQPNPD
WRYSASLRAG MHSSVHLEEA GILRAGPGGP DQQWPTVSSA TPEPEAGEVS PPVGAGVNSN
SWTFKYGPGN PKQSGPGELP DKFIIPGSPA IISIRQEPTN SQIDKSDFIT FGKKEETKKK
KKKKKGNKTQ EKKEKGNSTT DNSDQ*

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

40 / 40

Last intron/exon boundary

1786

Theoretical NMD boundary in CDS

1696

Length of CDS

2058

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

26210

Chromosomal position

140882092

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:

5:140882092A>C_2_ENST00000394633

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 49|151 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA1

Gene constraints

LOEUF: 0.88, LOF (oe): 0.65, misssense (oe): 0.94, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000394633.7

Genbank transcript ID

NM_031411 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1602+94200A>C
g.95957A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQPRQPNP
DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS
NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI TFGKKEETKK
KKKKKKGNKT QEKKEKGNST TDNSDQ*

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

1 / 1

Last intron/exon boundary

1750

Theoretical NMD boundary in CDS

1699

Length of CDS

2061

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

95957

Chromosomal position

140882092

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:

5:140882092A>C_12_ENST00000307360

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 49|151 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA10

Gene constraints

LOEUF: 0.91, LOF (oe): 0.71, misssense (oe): 0.99, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000307360.6

Genbank transcript ID

NM_018901 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2388+23656A>C
g.26210A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVSRCSCLGV QCLLLSLLLL AAWEVGSGQL HYSVYEEARH GTFVGRIAQD LGLELAELVQ
RLFRVASKRH GDLLEVNLQN GILFVNSRID REELCGRSVE CSIHLEVIVD RPLQVFHVDV
EVKDINDNPP RFSVTEQKLS IPESRLLDSR FPLEGASDAD VGENALLTYK LSPNEYFVLD
IINKKDKDKF PVLVLRKLLD REENPQLKLL LTATDGGKPE FTGSVSLLIL VLDANDNAPI
FDRPVYEVKM YENQVNQTLV IRLNASDSDE GINKEMMYSF SSLVPPTIRR KFWINERTGE
IKVNDAIDFE DSNTYEIHVD VTDKGNPPMV GHCTVLVELL DENDNSPEVI VTSLSLPVKE
DAQVGTVIAL ISVSDHDSGA NGQVTCSLTP HVPFKLVSTY KNYYSLVLDS ALDRERVSAY
ELVVTARDGG SPPLWATASV SVEVADVNDN APAFAQSEYT VFVKENNPPG CHIFTVSAWD
ADAQENALVS YSLVERRLGE RSLSSYVSVH AESGKVYALQ PLDHEELELL QFQVSARDGG
VPPLGSNLTL QVFVLDENDN APALLASPAG SAGGAVSELV LRSVVAGHVV AKVRAVDADS
GYNAWLSYEL QSAAVGARIP FRVGLYTGEI STTRALDETD SPRQRLLVLV KDHGEPSLTA
TATVLVSLVE GSQAPKASSR ASVGVAPEVA LVDVNVYLII AICAVSSLLV LTLLLYTALR
CSAAPTEGAC GPVKPTLVCS SAVGSWSYSQ QRRQRVCSGE GLPKADLMAF SPSLPPCPMV
DVDGEDQSIG GDHSRKPRQP NPDWRYSASL RAGMHSSVHL EEAGILRAGP GGPDQQWPTV
SSATPEPEAG EVSPPVGAGV NSNSWTFKYG PGNPKQSGPG ELPDKFIIPG SPAIISIRQE
PTNSQIDKSD FITFGKKEET KKKKKKKKGN KTQEKKEKGN STTDNSDQ*

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

153 / 153

Last intron/exon boundary

2688

Theoretical NMD boundary in CDS

2485

Length of CDS

2847

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

26210

Chromosomal position

140882092

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:

5:140882092A>C_16_ENST00000530339

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 49|151 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA4

Gene constraints

LOEUF: 0.98, LOF (oe): 0.77, misssense (oe): 0.97, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000530339.2

Genbank transcript ID

NM_018907 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2385+72520A>C
g.75056A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEFSWGSGQE SRRLLLLLLL LAAWEAGNGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKG RGGLLEVNLQ NGILFVNSRI DREELCRRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PVFPATQKNL SIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFSL
EKPPDDELVK GLGLILRKSL DREEAPEIFL VLTATDGGKP ELTGTVQLLI TVLDANDNAP
AFDRTIYKVR LLENVPNGTL VIKLNASDLD EGLNGDIVYS FSNDISPNVK SKFHIDPITG
QIIVKGYIDF EESKSYEIIV EGIDKGQLPL SGHCRVIVEV EDNNDNVPDL EFKSLSLPIR
EDAPLGTVIA LISVSDKDMG VNGLVTCSLT SHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVTARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GGTGGAVSEL VPWSVGVGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDET DAPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RALVGAVGPD AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSALPTEG ACAPGKPTLV CSSAVGSWSY SQQRRPRVCS GEGPPKTDLM AFSPSLPDSR
DREDQLQTTE ESFAKPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS
SATPEPEAGE VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP
TNSQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ*

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

121 / 121

Last intron/exon boundary

2653

Theoretical NMD boundary in CDS

2482

Length of CDS

2844

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

75056

Chromosomal position

140882092

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:

5:140882092A>C_1_ENST00000504120

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 50|150 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA1

Gene constraints

LOEUF: 0.85, LOF (oe): 0.66, misssense (oe): 0.96, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000504120.4

Genbank transcript ID

NM_018900 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2394+93408A>C
g.95957A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL
NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

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

152 / 152

Last intron/exon boundary

2693

Theoretical NMD boundary in CDS

2491

Length of CDS

2853

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

95957

Chromosomal position

140882092

Speed

0.04 s

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

Back to summary table

MutationT@ster 2025

Variant:

5:140882092A>C_17_ENST00000512229

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 51|149 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA4

Gene constraints

LOEUF: 1.03, LOF (oe): 0.82, misssense (oe): 0.98, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000512229.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2385+72520A>C
g.75056A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MEFSWGSGQE SRRLLLLLLL LAAWEAGNGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKG RGGLLEVNLQ NGILFVNSRI DREELCRRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PVFPATQKNL SIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFSL
EKPPDDELVK GLGLILRKSL DREEAPEIFL VLTATDGGKP ELTGTVQLLI TVLDANDNAP
AFDRTIYKVR LLENVPNGTL VIKLNASDLD EGLNGDIVYS FSNDISPNVK SKFHIDPITG
QIIVKGYIDF EESKSYEIIV EGIDKGQLPL SGHCRVIVEV EDNNDNVPDL EFKSLSLPIR
EDAPLGTVIA LISVSDKDMG VNGLVTCSLT SHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVTARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GGTGGAVSEL VPWSVGVGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDET DAPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RALVGAVGPD AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSALPTEG ACAPGKPTLV CSSAVGSWSY SQQRRPRVCS GEGPPKTDLM AFSPSLPDSR
DREDQLQTTE ESFAKPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS
SATPEPEAGE VSPPVGAGVN SNSWTFKYGP GNPKQSGPEP KKQTQVSFLL RRKGEASQPR
Q*

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

115 / 115

Last intron/exon boundary

2749

Theoretical NMD boundary in CDS

2584

Length of CDS

2706

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

75056

Chromosomal position

140882092

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:

5:140882092A>C_9_ENST00000525929

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 52|148 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA7

Gene constraints

LOEUF: 0.86, LOF (oe): 0.65, misssense (oe): 1.00, synonymous (oe): 1.04 ? (gnomAD)

Ensembl transcript ID

ENST00000525929.2

Genbank transcript ID

NM_018910 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2355+45354A>C
g.47845A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVCPNGYDPG GRHLLLFIII LAAWEAGRGQ LHYSVPEEAK HGNFVGRIAQ DLGLELAELV
PRLFRAVCKF RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV ERPLQVFHVD
VEVKDINDNP PVFPATQRNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTVLVEV VDVNDNAPQL TLTSLSLPIP
EDAQPGTVIT LISVFDRDFG VNGQVTCSLT PRVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAG
DADAQKNALV SYSLVELRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTGGAVREL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPVAAGASI PFRVGLYTGE ISTTRALDET DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS RASLGIAGPE TELVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSAPSSEG ACSLVKPTLV CSSAVGSWSF SQQRRQRVCS GEGPPKTDLM AFSPSLPQGP
SSTDNPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS SATPEPEAGE
VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP TNSQIDKSDF
ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ*

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

116 / 116

Last intron/exon boundary

2618

Theoretical NMD boundary in CDS

2452

Length of CDS

2814

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

47845

Chromosomal position

140882092

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:

5:140882092A>C_15_ENST00000398631

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 53|147 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA12

Gene constraints

LOEUF: 0.93, LOF (oe): 0.72, misssense (oe): 0.98, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000398631.3

Genbank transcript ID

NM_018903 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2367+4253A>C
g.6791A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVIIGPRGPG SQRLLLSLLL LAAWEVGSGQ LHYSVYEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREKLCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFREREQKV PVSESAPLDS HFPLEGASDA DIGVNSLLTY ALSLNENFEL
KIKTKKDKSI LPELVLRKLL DREQTPKLNL LLMVIDGGKP ELTGSVQIQI TVLDVNDNGP
AFDKPSYKVV LSENVQNDTR VIQLNASDPD EGLNGEISYG IKMILPVSEK CMFSINPDTG
EIRIYGELDF EENNAYEIQV NAIDKGIPSM AGHSMVLVEV LDVNDNVPEV MVTSLSLPVQ
EDAQVGTVIA LISVSDRDSG ANGQVICSLT PHVPFKLVST YKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQKNALV SYSLVERRVG EHALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLATPA GSAGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPAAVGAHI PFHVGLYTGE ISTTRILDEA DAPRHRLLVL VKDHGEPALT
STATVLVSLV ENGQAPKTSS RASVGAVDPE AALVDINVYL IIAICAVSSL LVLTLLLYTA
LRCSAPPTVS RCAPGKPTLV CSSAVGSWSY SQQRRQRVCS AESPPKTDLM AFSPSLQLSR
EDCLNPPSEP RQPNPDWRYS ASLRAGMHSS VHLEEAGILR AGPGGPDQQW PTVSSATPEP
EAGEVSPPVG AGVNSNSWTF KYGPGNPKQS GPGELPDKFI IPGSPAIISI RQEPTNSQID
KSDFITFGKK EETKKKKKKK KGNKTQEKKE KGNSTTDNSD Q*

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

166 / 166

Last intron/exon boundary

2680

Theoretical NMD boundary in CDS

2464

Length of CDS

2826

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

6791

Chromosomal position

140882092

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:

5:140882092A>C_4_ENST00000522353

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 54|146 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA3

Gene constraints

LOEUF: 0.81, LOF (oe): 0.63, misssense (oe): 0.99, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000522353.3

Genbank transcript ID

NM_018906 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2394+78501A>C
g.81065A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLFSWREDPG AQCLLLSLLL LAASEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVE
VEVKDINDNA PVFPMAVKNL FISESRQPGS RFSLEGASDA DIGTNSLLTY SLDSTEYFTL
DVKRNDEEIK SLGLVLKKNL NREDTPKHYL LITAIDGGKP ELTGTTQLKI TVLDVNDNAP
AFERTIYKVR LLENAPNGTL VVTVNATDLD EGVNKDIAYS FNTDMSADIL SKFHLDPVNG
QISVKGNIDF EESKSYEIQV EATDKGNPPM SDHCTVLLEI VDINDNVPEL VIQSLSLPVL
EDSPLSTVIA LISVSDRDSG VNGQVTCSLT PHVPFKLVST FKNYYSLVLD SPLDRESVSA
YELVVTARDG GSPSLWATAS VSVEVADVND NAPAFSQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLMPRV GGIGGAVSEL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDEV DAPRHRLLVL VKDHGEPSLT
ATATVLVSLV ESGQAPKASS QASAGATGPE AALVDVNVYL IVAICAVSSL LVLTLLLYTA
LRCSAPPTEG DCGPGKPTLV CSSAVGSWSY SQQRQQRVCS GEGLPKTDLM AFSPSLPPCP
ISRDREEKQD VDVDLSAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

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

142 / 142

Last intron/exon boundary

2683

Theoretical NMD boundary in CDS

2491

Length of CDS

2853

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

81065

Chromosomal position

140882092

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:

5:140882092A>C_8_ENST00000527624

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 54|146 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA6

Gene constraints

LOEUF: 1.03, LOF (oe): 0.79, misssense (oe): 0.97, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000527624.1

Genbank transcript ID

NM_031849 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1602+52399A>C
g.54135A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PLFPVEEQRV LIYESRLPDS VFPLEGASDA DVGSNSILTY KLSSSEYFGL
DVKINSDDNK QIGLLLKKSL DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
TFEQSEYEVR IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS LSVEVADMND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQPRQPNP
DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS
NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI TFGKKEETKK
KKKKKKGNKT QEKKEKGNST TDNSDQ*

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

28 / 28

Last intron/exon boundary

1777

Theoretical NMD boundary in CDS

1699

Length of CDS

2061

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

54135

Chromosomal position

140882092

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:

5:140882092A>C_10_ENST00000531613

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 54|146 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA8

Gene constraints

LOEUF: 1.04, LOF (oe): 0.82, misssense (oe): 1.01, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000531613.2

Genbank transcript ID

NM_018911 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2394+38377A>C
g.40906A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MDYHWRGELG SWRLLLLLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
PRLFRVASKR HRDLLEVSLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDVNDNP PVFRVKDQKL FVSESRMPDS RFPLEGASDA DVGANSVLTY RLSSHDYFML
DVNSKNDENK LVELVLRKSL DREDAPAHHL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
TFEQSEYEVR IFENADNGTT VIKLNASDPD EGANGAISYS FNSLVETMVI DHFSIDRNTG
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
EDAQFGTVIA LISVNDLDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRERVSA
YELVVTARDG GSPSLWATAS LSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERSLSSYISV HTESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLEPRV GGTGGAASKL VPRSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQPAASSPRI PFRVGLYTGE ISTTRVLDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RQSAGVLGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSALPTEG GCRAGKPTLV CSSAVGSWSY SQQQPQRVCS GEGPPKTDLM AFSPCLPPDL
GSVDVGEEQD LNVDHGLKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

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

136 / 136

Last intron/exon boundary

2677

Theoretical NMD boundary in CDS

2491

Length of CDS

2853

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

40906

Chromosomal position

140882092

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:

5:140882092A>C_5_ENST00000529859

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 55|145 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA5

Gene constraints

LOEUF: 0.87, LOF (oe): 0.67, misssense (oe): 1.01, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000529859.2

Genbank transcript ID

NM_018908 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2352+57965A>C
g.60489A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVYSRRGSLG SRLLLLWLLL AYWKAGSGQL HYSIPEEAKH GTFVGRIAQD LGLELAELVP
RLFRVASKGR GDLLEVNLQN GILFVNSRID REELCRRRAE CSIHLEVIVD RPLQVFHVEV
AVKDINDNPP RFSRQEQRLF ILESRMPDSR FPLEGASDLD IGANAQLRYR LNPNEYFDLD
VKTNEEETNF LELVLRKSLD REETQEHRLL VIATDGGKPE LTGTVQLLIN VLDANDNAPE
FDKSIYNVRL LENAPSGTLV IKLNASDADE GINKEIVYFF SNLVLDDVKS KFIINSNTGE
IKVNGELDYE DYNSYEINID AMDKSTFPLS GHCKVVVKLL DVNDNTPEMA ITTLFLPVKE
DAPLSTVIAL ISVSDRDSGA NGQVTCSLMP HVPFKLVSTF KNYYSLVLDS ALDRESVSVY
ELVVTARDGG SPSLWATASV SVEVADVNDN APAFAQPQYT VFVKENNPPG CHIFTVSARD
ADAQENALVS YSLVERRVGE RPLSSYVSVH AESGKVYALQ PLDHEEVELL QFQVSARDAG
VPPLGSNVTL QVFVLDENDN APALLVPRVG GTGGAVSELV PRSVGAGHVV AKVRAVDPDS
GYNAWLSYEL QPAPGSARIP FRVGLYTGEI STTRSLDETE APRHRLLVLV KDHGEPPLTA
TATVLVSLVE SGQAPKASSR ASAGAVGPEA ALVDVNVYLI IAICAVSSLL VLTLLLYTAL
RCSAQPTEAV CTRGKPTLLC SSAVGSWSYS QQRRQRVCSG EAPPKTDLMA FSPSLPQGPT
STDNPRQPNP DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV
SPPVGAGVNS NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI
TFGKKEETKK KKKKKKGNKT QEKKEKGNST TDNSDQ*

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

164 / 164

Last intron/exon boundary

2663

Theoretical NMD boundary in CDS

2449

Length of CDS

2811

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

60489

Chromosomal position

140882092

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:

5:140882092A>C_3_ENST00000526136

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 56|144 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA2

Gene constraints

LOEUF: 1.05, LOF (oe): 0.85, misssense (oe): 0.96, synonymous (oe): 1.08 ? (gnomAD)

Ensembl transcript ID

ENST00000526136.2

Genbank transcript ID

NM_018905 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2388+84740A>C
g.87241A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MASSIRRGRG AWTRLLSLLL LAAWEVGSGQ LRYSVPEEAK HGTFVGRIAQ DLGLELEELV
PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHVEVIV DRPLQVFHVE
VEVKDINDNP PIFPMTVKTI RFPESRLLDS RFPLEGASDA DIGVNALLSY KLSSSEFFFL
DIQANDELSE SLSLVLGKSL DREETAEVNL LLVATDGGKP ELTGTVQILI KVLDVNDNEP
TFAQSVYKVK LLENTANGTL VVKLNASDAD EGPNSEIVYS LGSDVSSTIQ TKFTIDPISG
EIRTKGKLDY EEAKSYEIQV TATDKGTPSM SGHCKISLKL VDINDNTPEV SITSLSLPIS
ENASLGTVIA LITVSDRDSG TNGHVTCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATTS VSIEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEEVEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRA GTAAGAVSEL VPWSVGAGHV VAKVRAVDAD
SGYNAWLSYE LQLGTGSARI PFRVGLYTGE ISTTRALDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RAWVGAAGSE ATLVDVNVYL IIAICAVSSL LVLTVLLYTA
LRCSVPPTEG ARAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEDPPKTDLM AFSPSLSQGP
DSAEEKQLSE SEYVGKPRQP NPDWRYSASL RAGMHSSVHL EEAGILRAGP GGPDQQWPTV
SSATPEPEAG EVSPPVGAGV NSNSWTFKYG PGNPKQSGPG ELPDKFIIPG SPAIISIRQE
PTNSQIDKSD FITFGKKEET KKKKKKKKGN KTQEKKEKGN STTDNSDQ*

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

114 / 114

Last intron/exon boundary

2649

Theoretical NMD boundary in CDS

2485

Length of CDS

2847

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

87241

Chromosomal position

140882092

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:

5:140882092A>C_14_ENST00000398640

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 57|143 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA11

Gene constraints

LOEUF: 1.03, LOF (oe): 0.83, misssense (oe): 1.01, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000398640.7

Genbank transcript ID

NM_018902 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2391+10598A>C
g.13910A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MFGFQRRGLG TPRLQLWLLL LEFWEVGSGQ LHYSVSEEAK HGTFVGRIAQ DLGLELAELV
QRLFRVASKT HGDLLEVNLQ NGILFVNSRI DREELCGQSA ECSIHLEVIV DRPLQVFHVN
VEVKDINDNP PVFSLREQKL LIAESKQSDS RFPLEGASDA DIEENALLTY RLSKNEYFSL
DSPTNGKQIK RLSLILKKSL DREKTPELNL LLTATDGGKP ELTGTVRLLV QVLDVNDNDP
EFDKSEYKVS LMENAAKETL VLKLNATDRD EGVNGEVTYS LMSIKPNGRH LFTLDQNNGE
VRVNGTLDYE ENKFYKIEVQ ATDKGTPPMA GHCTVWVEIL DTNDNSPEVA VTSLSLPVRE
DAQPSTVIAL ISVSDRDSGV NGQVTCSLTP HVPFKLVSTF KNYYSLVLDS ALDRENVWAY
ELVVTARDGG SPSLWATARV SVEVADVNDN APAFAQPEYT VFVKENNPPG CHIFTVSARD
ADAQENALVS YSLVERRLGD RALSSYVSVH AESGKVYALQ PLDHEELELL QFQVSARDAG
VPPLSSNVTL QVFVLDENDN APALLATQAG SAGGAVNKLV PRSVGAGHVV AKVRAVDADS
GYNAWLSYEL QPAAGGSRIP FRVGLYTGEI STTRALDEAD SPRHRLLVLV KDHGEPALTA
TATVLVSLVE SGQAPKASSR TLAGAASPEA ALVDVNVYLI IAICVVSSLL VLTLLLYTAL
WWSATPTEGA CAPGKPTLVC SRAVGSWSYS QQRRQRVCSE EGPPKTDLMA FSPSLPLGLN
KEEEGERQEP GSNHPGQPRQ PNPDWRYSAS LRAGMHSSVH LEEAGILRAG PGGPDQQWPT
VSSATPEPEA GEVSPPVGAG VNSNSWTFKY GPGNPKQSGP GELPDKFIIP GSPAIISIRQ
EPTNSQIDKS DFITFGKKEE TKKKKKKKKG NKTQEKKEKG NSTTDNSDQ*

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

148 / 148

Last intron/exon boundary

2686

Theoretical NMD boundary in CDS

2488

Length of CDS

2850

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

13910

Chromosomal position

140882092

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:

5:140882092A>C_6_ENST00000529619

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 66|134 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA5

Gene constraints

LOEUF: 0.92, LOF (oe): 0.72, misssense (oe): 1.02, synonymous (oe): 1.10 ? (gnomAD)

Ensembl transcript ID

ENST00000529619.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2352+57965A>C
g.60489A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVYSRRGSLG SRLLLLWLLL AYWKAGSGQL HYSIPEEAKH GTFVGRIAQD LGLELAELVP
RLFRVASKGR GDLLEVNLQN GILFVNSRID REELCRRRAE CSIHLEVIVD RPLQVFHVEV
AVKDINDNPP RFSRQEQRLF ILESRMPDSR FPLEGASDLD IGANAQLRYR LNPNEYFDLD
VKTNEEETNF LELVLRKSLD REETQEHRLL VIATDGGKPE LTGTVQLLIN VLDANDNAPE
FDKSIYNVRL LENAPSGTLV IKLNASDADE GINKEIVYFF SNLVLDDVKS KFIINSNTGE
IKVNGELDYE DYNSYEINID AMDKSTFPLS GHCKVVVKLL DVNDNTPEMA ITTLFLPVKE
DAPLSTVIAL ISVSDRDSGA NGQVTCSLMP HVPFKLVSTF KNYYSLVLDS ALDRESVSVY
ELVVTARDGG SPSLWATASV SVEVADVNDN APAFAQPQYT VFVKENNPPG CHIFTVSARD
ADAQENALVS YSLVERRVGE RPLSSYVSVH AESGKVYALQ PLDHEEVELL QFQVSARDAG
VPPLGSNVTL QVFVLDENDN APALLVPRVG GTGGAVSELV PRSVGAGHVV AKVRAVDPDS
GYNAWLSYEL QPAPGSARIP FRVGLYTGEI STTRSLDETE APRHRLLVLV KDHGEPPLTA
TATVLVSLVE SGQAPKASSR ASAGAVGPEA ALVDVNVYLI IAICAVSSLL VLTLLLYTAL
RCSAQPTEAV CTRGKPTLLC SSAVGSWSYS QQRRQRVCSG EAPPKTDLMA FSPSLPQGPT
STDNPRQPNP DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV
SPPVGAGVNS NSWTFKYGPG NPKQSGPEPK KQTQVSFLLR RKGEASQPRQ *

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

2741

Theoretical NMD boundary in CDS

2551

Length of CDS

2673

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

60489

Chromosomal position

140882092

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:

5:140882092A>C_7_ENST00000529310

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 73|127 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA6

Gene constraints

LOEUF: 1.09, LOF (oe): 0.87, misssense (oe): 1.01, synonymous (oe): 1.13 ? (gnomAD)

Ensembl transcript ID

ENST00000529310.6

Genbank transcript ID

NM_018909 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2394+51607A>C
g.54135A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PLFPVEEQRV LIYESRLPDS VFPLEGASDA DVGSNSILTY KLSSSEYFGL
DVKINSDDNK QIGLLLKKSL DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
TFEQSEYEVR IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS LSVEVADMND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTGGAVSEL VPRSLGAGQV VAKVRAVDAD
SGYNAWLSYE LQPPASSARF PFRVGLYTGE ISTTRVLDEA DSPRHRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKASS RASVGAAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
LRCSAPPTEG ACTADKPTLV CSSAVGSWSY SQQRRQRVCS GEGPPKMDLM AFSPSLSPCP
IMMGKAENQD LNEDHDAKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

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

133 / 133

Last intron/exon boundary

2674

Theoretical NMD boundary in CDS

2491

Length of CDS

2853

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

54135

Chromosomal position

140882092

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:

5:140882092A>C_11_ENST00000532602

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 82|118 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr5:140882092A>C (GRCh38)

Gene symbol

PCDHA9

Gene constraints

LOEUF: 1.23, LOF (oe): 0.99, misssense (oe): 0.99, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000532602.2

Genbank transcript ID

NM_031857 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.2394+31203A>C
g.34321A>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	rs59479
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.501	0.014
	6.003	0.591
(flanking)	0.289	0.016

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

5

Strand

1

Original gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGAACGTTTCCGCGAAGAAAGCC

Altered gDNA sequence snippet

TGGTGTCGCTCTTCACTGAGCACGTTTCCGCGAAGAAAGCC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MLYSSRGDPE GQPLLLSLLI LAMWVVGSGQ LHYSVPEEAE HGTFVGRIAQ DLGLELAELV
PRLFQLDSKG RGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVKDINDNP PVFPATQKNL FIAESRPLDS RFPLEGASDA DIGENALLTY RLSPNEYFFL
DVPTSNQQVK PLGLVLRKLL DREETPELHL LLTATDGGKP ELTGTVQLLI TVLDNNDNAP
VFDRTLYTVK LPENVSIGTL VIHPNASDLD EGLNGDIIYS FSSDVSPDIK SKFHMDPLSG
AITVIGHMDF EESRAHKIPV EAVDKGFPPL AGHCTLLVEV VDVNDNAPQL TIKTLSVPVK
EDAQLGTVIA LISVIDLDAD ANGQVTCSLT PHVPFKLVST YKNYYSLVLD RALDRESVSA
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQSEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRLG ERSLSSYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
GVPPLGSNVT LQVFVLDEND NAPALLTPRM RGTDGAVSEM VLRSVGAGVV VGKVRAVDAD
SGYNAWLSYE LQPETASASI PFRVGLYTGE ISTTRALDET DAPRQRLLVL VKDHGEPALT
ATATVLVSLV ESGQAPKSSS RASVGATGPE VTLVDVNVYL IIAICAVSSL LVLTLLLYTV
LRCSAMPTEG ECAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEGKQKTDLM AFSPGLSPCA
GSTERTGEPS ASSDSTGKPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ *

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

115 / 115

Last intron/exon boundary

2656

Theoretical NMD boundary in CDS

2491

Length of CDS

2853

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

34321

Chromosomal position

140882092

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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