MutationT @ ster 2025

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 73|27 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.40, LOF (oe): 0.26, misssense (oe): 0.82, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000361548.9

Genbank transcript ID

NM_198173 (exact from MANE)

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1795C>G
g.154917C>G

AA changes

AAE:	L599V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		599	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	599	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no alignment	n/a
Mmulatta	no alignment	n/a
Fcatus	all identical	599	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L
Mmusculus	all identical	600	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L
Ggallus	all identical	626	M	V	E	A	E	D	K	I	Q	V	I	L	K	E	L
Trubripes	all identical	566									Q	V	T	L	A	E	V
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	591												L	K	E	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MSNELDFRSV RLLKNDPVNL QKFSYTSEDE AWKTYLENPL TAATKAMMRV NGDDDSVAAL
SFLYDYYMGP KEKRILSSST GGRNDQGKRY YHGMEYETDL TPLESPTHLM KFLTENVSGT
PEYPDLLKKN NLMSLEGALP TPGKAAPLPA GPSKLEAGSV DSYLLPTTDM YDNGSLNSLF
ESIHGVPPTQ RWQPDSTFKD DPQESMLFPD ILKTSPEPPC PEDYPSLKSD FEYTLGSPKA
IHIKSGESPM AYLNKGQFYP VTLRTPAGGK GLALSSNKVK SVVMVVFDNE KVPVEQLRFW
KHWHSRQPTA KQRVIDVADC KENFNTVEHI EEVAYNALSF VWNVNEEAKV FIGVNCLSTD
FSSQKGVKGV PLNLQIDTYD CGLGTERLVH RAVCQIKIFC DKGAERKMRD DERKQFRRKV
KCPDSSNSGV KGCLLSGFRG NETTYLRPET DLETPPVLFI PNVHFSSLQR SGGAAPSAGP
SSSNRLPLKR TCSPFTEEFE PLPSKQAKEG DLQRVLLYVR RETEEVFDAL MLKTPDLKGL
RNAISEKYGF PEENIYKVYK KCKRGILVNM DNNIIQHYSN HVAFLLDMGE LDGKIQIILK
EL*

Mutated AA sequence

MSNELDFRSV RLLKNDPVNL QKFSYTSEDE AWKTYLENPL TAATKAMMRV NGDDDSVAAL
SFLYDYYMGP KEKRILSSST GGRNDQGKRY YHGMEYETDL TPLESPTHLM KFLTENVSGT
PEYPDLLKKN NLMSLEGALP TPGKAAPLPA GPSKLEAGSV DSYLLPTTDM YDNGSLNSLF
ESIHGVPPTQ RWQPDSTFKD DPQESMLFPD ILKTSPEPPC PEDYPSLKSD FEYTLGSPKA
IHIKSGESPM AYLNKGQFYP VTLRTPAGGK GLALSSNKVK SVVMVVFDNE KVPVEQLRFW
KHWHSRQPTA KQRVIDVADC KENFNTVEHI EEVAYNALSF VWNVNEEAKV FIGVNCLSTD
FSSQKGVKGV PLNLQIDTYD CGLGTERLVH RAVCQIKIFC DKGAERKMRD DERKQFRRKV
KCPDSSNSGV KGCLLSGFRG NETTYLRPET DLETPPVLFI PNVHFSSLQR SGGAAPSAGP
SSSNRLPLKR TCSPFTEEFE PLPSKQAKEG DLQRVLLYVR RETEEVFDAL MLKTPDLKGL
RNAISEKYGF PEENIYKVYK KCKRGILVNM DNNIIQHYSN HVAFLLDMGE LDGKIQIIVK
EL*

Position of stopcodon in wt / mu CDS

1809 / 1809

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

603 / 603

Position of stopcodon in wt / mu cDNA

2004 / 2004

Position of start ATG in wt / mu cDNA

196 / 196

Last intron/exon boundary

1889

Theoretical NMD boundary in CDS

1643

Length of CDS

1809

Coding sequence (CDS) position

1795

cDNA position

1990

gDNA position

154917

Chromosomal position

24354474

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

MutationT@ster 2025

Variant:

1:24354474C>G_1_ENST00000528064

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.42, LOF (oe): 0.26, misssense (oe): 0.80, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000528064.6

Genbank transcript ID

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1516C>G
g.154917C>G

AA changes

AAE:	L506V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		506	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	506	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAA

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAA

Wildtype AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIILKEL*

Mutated AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIIVKEL*

Position of stopcodon in wt / mu CDS

1530 / 1530

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

510 / 510

Position of stopcodon in wt / mu cDNA

1683 / 1683

Position of start ATG in wt / mu cDNA

154 / 154

Last intron/exon boundary

1568

Theoretical NMD boundary in CDS

1364

Length of CDS

1530

Coding sequence (CDS) position

1516

cDNA position

1669

gDNA position

154917

Chromosomal position

24354474

Speed

0.13 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_2_ENST00000690803

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.42, LOF (oe): 0.26, misssense (oe): 0.80, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000690803.1

Genbank transcript ID

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1516C>G
g.154917C>G

AA changes

AAE:	L506V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		506	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	506	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIILKEL*

Mutated AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIIVKEL*

Position of stopcodon in wt / mu CDS

1530 / 1530

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

510 / 510

Position of stopcodon in wt / mu cDNA

1827 / 1827

Position of start ATG in wt / mu cDNA

298 / 298

Last intron/exon boundary

1712

Theoretical NMD boundary in CDS

1364

Length of CDS

1530

Coding sequence (CDS) position

1516

cDNA position

1813

gDNA position

154917

Chromosomal position

24354474

Speed

0.12 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_3_ENST00000692334

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 79|21 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.42, LOF (oe): 0.26, misssense (oe): 0.80, synonymous (oe): 0.99 ? (gnomAD)

Ensembl transcript ID

ENST00000692334.1

Genbank transcript ID

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1516C>G
g.154917C>G

AA changes

AAE:	L506V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		506	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	506	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIILKEL*

Mutated AA sequence

MEYETDLTPL ESPTHLMKFL TENVSGTPEY PDLLKKNNLM SLEGALPTPG KAAPLPAGPS
KLEAGSVDSY LLPTTDMYDN GSLNSLFESI HGVPPTQRWQ PDSTFKDDPQ ESMLFPDILK
TSPEPPCPED YPSLKSDFEY TLGSPKAIHI KSGESPMAYL NKGQFYPVTL RTPAGGKGLA
LSSNKVKSVV MVVFDNEKVP VEQLRFWKHW HSRQPTAKQR VIDVADCKEN FNTVEHIEEV
AYNALSFVWN VNEEAKVFIG VNCLSTDFSS QKGVKGVPLN LQIDTYDCGL GTERLVHRAV
CQIKIFCDKG AERKMRDDER KQFRRKVKCP DSSNSGVKGC LLSGFRGNET TYLRPETDLE
TPPVLFIPNV HFSSLQRSGG AAPSAGPSSS NRLPLKRTCS PFTEEFEPLP SKQAKEGDLQ
RVLLYVRRET EEVFDALMLK TPDLKGLRNA ISEKYGFPEE NIYKVYKKCK RGILVNMDNN
IIQHYSNHVA FLLDMGELDG KIQIIVKEL*

Position of stopcodon in wt / mu CDS

1530 / 1530

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

510 / 510

Position of stopcodon in wt / mu cDNA

1750 / 1750

Position of start ATG in wt / mu cDNA

221 / 221

Last intron/exon boundary

1635

Theoretical NMD boundary in CDS

1364

Length of CDS

1530

Coding sequence (CDS) position

1516

cDNA position

1736

gDNA position

154917

Chromosomal position

24354474

Speed

0.08 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_9_ENST00000236255

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 81|19 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.41, LOF (oe): 0.27, misssense (oe): 0.82, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000236255.4

Genbank transcript ID

NM_021180 (by similarity)

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1810C>G
g.154917C>G

AA changes

AAE:	L604V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		604	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	604									Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAA

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAA

Wildtype AA sequence

MWMNSILPIF LFRSVRLLKN DPVNLQKFSY TSEDEAWKTY LENPLTAATK AMMRVNGDDD
SVAALSFLYD YYMGPKEKRI LSSSTGGRND QGKRYYHGME YETDLTPLES PTHLMKFLTE
NVSGTPEYPD LLKKNNLMSL EGALPTPGKA APLPAGPSKL EAGSVDSYLL PTTDMYDNGS
LNSLFESIHG VPPTQRWQPD STFKDDPQES MLFPDILKTS PEPPCPEDYP SLKSDFEYTL
GSPKAIHIKS GESPMAYLNK GQFYPVTLRT PAGGKGLALS SNKVKSVVMV VFDNEKVPVE
QLRFWKHWHS RQPTAKQRVI DVADCKENFN TVEHIEEVAY NALSFVWNVN EEAKVFIGVN
CLSTDFSSQK GVKGVPLNLQ IDTYDCGLGT ERLVHRAVCQ IKIFCDKGAE RKMRDDERKQ
FRRKVKCPDS SNSGVKGCLL SGFRGNETTY LRPETDLETP PVLFIPNVHF SSLQRSGGAA
PSAGPSSSNR LPLKRTCSPF TEEFEPLPSK QAKEGDLQRV LLYVRRETEE VFDALMLKTP
DLKGLRNAIS EKYGFPEENI YKVYKKCKRG ILVNMDNNII QHYSNHVAFL LDMGELDGKI
QIILKEL*

Mutated AA sequence

MWMNSILPIF LFRSVRLLKN DPVNLQKFSY TSEDEAWKTY LENPLTAATK AMMRVNGDDD
SVAALSFLYD YYMGPKEKRI LSSSTGGRND QGKRYYHGME YETDLTPLES PTHLMKFLTE
NVSGTPEYPD LLKKNNLMSL EGALPTPGKA APLPAGPSKL EAGSVDSYLL PTTDMYDNGS
LNSLFESIHG VPPTQRWQPD STFKDDPQES MLFPDILKTS PEPPCPEDYP SLKSDFEYTL
GSPKAIHIKS GESPMAYLNK GQFYPVTLRT PAGGKGLALS SNKVKSVVMV VFDNEKVPVE
QLRFWKHWHS RQPTAKQRVI DVADCKENFN TVEHIEEVAY NALSFVWNVN EEAKVFIGVN
CLSTDFSSQK GVKGVPLNLQ IDTYDCGLGT ERLVHRAVCQ IKIFCDKGAE RKMRDDERKQ
FRRKVKCPDS SNSGVKGCLL SGFRGNETTY LRPETDLETP PVLFIPNVHF SSLQRSGGAA
PSAGPSSSNR LPLKRTCSPF TEEFEPLPSK QAKEGDLQRV LLYVRRETEE VFDALMLKTP
DLKGLRNAIS EKYGFPEENI YKVYKKCKRG ILVNMDNNII QHYSNHVAFL LDMGELDGKI
QIIVKEL*

Position of stopcodon in wt / mu CDS

1824 / 1824

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

608 / 608

Position of stopcodon in wt / mu cDNA

1870 / 1870

Position of start ATG in wt / mu cDNA

47 / 47

Last intron/exon boundary

1755

Theoretical NMD boundary in CDS

1658

Length of CDS

1824

Coding sequence (CDS) position

1810

cDNA position

1856

gDNA position

154917

Chromosomal position

24354474

Speed

0.15 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_4_ENST00000689444

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.40, LOF (oe): 0.25, misssense (oe): 0.81, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000689444.1

Genbank transcript ID

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1657C>G
g.154917C>G

AA changes

AAE:	L553V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		553	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	553	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IILKEL*

Mutated AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IIVKEL*

Position of stopcodon in wt / mu CDS

1671 / 1671

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

557 / 557

Position of stopcodon in wt / mu cDNA

1926 / 1926

Position of start ATG in wt / mu cDNA

256 / 256

Last intron/exon boundary

1811

Theoretical NMD boundary in CDS

1505

Length of CDS

1671

Coding sequence (CDS) position

1657

cDNA position

1912

gDNA position

154917

Chromosomal position

24354474

Speed

0.13 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_7_ENST00000356046

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.40, LOF (oe): 0.25, misssense (oe): 0.81, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000356046.6

Genbank transcript ID

NM_001195010 (by similarity)

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1657C>G
g.154917C>G

AA changes

AAE:	L553V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		553	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	553	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IILKEL*

Mutated AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IIVKEL*

Position of stopcodon in wt / mu CDS

1671 / 1671

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

557 / 557

Position of stopcodon in wt / mu cDNA

1974 / 1974

Position of start ATG in wt / mu cDNA

304 / 304

Last intron/exon boundary

1859

Theoretical NMD boundary in CDS

1505

Length of CDS

1671

Coding sequence (CDS) position

1657

cDNA position

1960

gDNA position

154917

Chromosomal position

24354474

Speed

0.13 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_8_ENST00000524724

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 82|18 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.40, LOF (oe): 0.25, misssense (oe): 0.81, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000524724.6

Genbank transcript ID

UniProt / AlphaMissense peptide

GRHL3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1657C>G
g.154917C>G

AA changes

AAE:	L553V	?
Score:	32

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		553	M	G	E	L	D	G	K	I	Q	I	I	L	K	E	L	*
mutated	all conserved	553	M	G	E	L	D	G	K	I	Q	I	I	V	K	E	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	626	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered cDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Wildtype AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IILKEL*

Mutated AA sequence

MMRVNGDDDS VAALSFLYDY YMGPKEKRIL SSSTGGRNDQ GKRYYHGMEY ETDLTPLESP
THLMKFLTEN VSGTPEYPDL LKKNNLMSLE GALPTPGKAA PLPAGPSKLE AGSVDSYLLP
TTDMYDNGSL NSLFESIHGV PPTQRWQPDS TFKDDPQESM LFPDILKTSP EPPCPEDYPS
LKSDFEYTLG SPKAIHIKSG ESPMAYLNKG QFYPVTLRTP AGGKGLALSS NKVKSVVMVV
FDNEKVPVEQ LRFWKHWHSR QPTAKQRVID VADCKENFNT VEHIEEVAYN ALSFVWNVNE
EAKVFIGVNC LSTDFSSQKG VKGVPLNLQI DTYDCGLGTE RLVHRAVCQI KIFCDKGAER
KMRDDERKQF RRKVKCPDSS NSGVKGCLLS GFRGNETTYL RPETDLETPP VLFIPNVHFS
SLQRSGGAAP SAGPSSSNRL PLKRTCSPFT EEFEPLPSKQ AKEGDLQRVL LYVRRETEEV
FDALMLKTPD LKGLRNAISE KYGFPEENIY KVYKKCKRGI LVNMDNNIIQ HYSNHVAFLL
DMGELDGKIQ IIVKEL*

Position of stopcodon in wt / mu CDS

1671 / 1671

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

557 / 557

Position of stopcodon in wt / mu cDNA

1920 / 1920

Position of start ATG in wt / mu cDNA

250 / 250

Last intron/exon boundary

1805

Theoretical NMD boundary in CDS

1505

Length of CDS

1671

Coding sequence (CDS) position

1657

cDNA position

1906

gDNA position

154917

Chromosomal position

24354474

Speed

0.08 s

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

MutationT@ster 2025

Variant:

1:24354474C>G_6_ENST00000350501

Prediction:

DeleteriousPermalink

Summary:

Known as potential disease variant: ClinVar ID 208652 (likely pathogenic)

Model: without_aae
Tree vote: 141|59 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr1:24354474C>G (GRCh38)

Gene symbol

Gene constraints

LOEUF: 0.39, LOF (oe): 0.25, misssense (oe): 0.84, synonymous (oe): 1.01 ? (gnomAD)

Ensembl transcript ID

ENST00000350501.9

Genbank transcript ID

NM_198174 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.1694+4352C>G
g.154917C>G

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Inborn genetic diseases

likely pathogenic

Variant DBs

	Not in dbSNP
	Allele 'G' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	2.158	1
	6.608	1
(flanking)	6.7	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

N/A

AA sequence altered

N/A

Chromosome

1

Strand

1

Original gDNA sequence snippet

ACGGCAAAATTCAGATCATCCTTAAGGAGCTGTAAGGCCTC

Altered gDNA sequence snippet

ACGGCAAAATTCAGATCATCGTTAAGGAGCTGTAAGGCCTC

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MSNELDFRSV RLLKNDPVNL QKFSYTSEDE AWKTYLENPL TAATKAMMRV NGDDDSVAAL
SFLYDYYMGP KEKRILSSST GGRNDQGKRY YHGMEYETDL TPLESPTHLM KFLTENVSGT
PEYPDLLKKN NLMSLEGALP TPGKAAPLPA GPSKLEAGSV DSYLLPTTDM YDNGSLNSLF
ESIHGVPPTQ RWQPDSTFKD DPQESMLFPD ILKTSPEPPC PEDYPSLKSD FEYTLGSPKA
IHIKSGESPM AYLNKGQFYP VTLRTPAGGK GLALSSNKVK SVVMVVFDNE KVPVEQLRFW
KHWHSRQPTA KQRVIDVADC KENFNTVEHI EEVAYNALSF VWNVNEEAKV FIGVNCLSTD
FSSQKGVKGV PLNLQIDTYD CGLGTERLVH RAVCQIKIFC DKGAERKMRD DERKQFRRKV
KCPDSSNSGV KGCLLSGFRG NETTYLRPET DLETPPVLFI PNVHFSSLQR SGGAAPSAGP
SSSNRLPLKR TCSPFTEEFE PLPSKQAKEG DLQRVLLYVR RETEEVFDAL MLKTPDLKGL
RNAISEKYGF PEENIYKVYK KCKRGETSLL HPRLSRHPPP DCLECSHPVT QVRNMGFGDG
FWRQRDLDSN PSPTTVNSLH FTVNSE*

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

128 / 128

Last intron/exon boundary

1821

Theoretical NMD boundary in CDS

1643

Length of CDS

1881

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

154917

Chromosomal position

24354474

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