MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000297261
MT speed 0.04 s - this script 2.505275 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000297261(MANE Select)	SHH	Deleterious	90\|10	simple_aae		No	Yes			Single base exchange		Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 8877 (pathogenic) Protein features (might be) affected

MutationT@ster 2025

Variant:

7:155812032C>T_1_ENST00000297261

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 8877 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 90|10 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr7:155812032C>T (GRCh38)

Gene symbol

SHH

Gene constraints

LOEUF: 0.49, LOF (oe): 0.21, misssense (oe): 0.94, synonymous (oe): 1.32 ? (gnomAD)

Ensembl transcript ID

ENST00000297261.7

Genbank transcript ID

NM_000193 (exact from MANE)

UniProt / AlphaMissense peptide

SHH_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.91G>A
g.432G>A

AA changes

AAE:	G31R	?
Score:	125

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Holoprosencephaly 3

pathogenic

ClinVar OMIM

Variant DBs

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

Protein conservation

Species	Match	AA	Alignment
Human		31	S	G	L	A	C	G	P	G	R	G	F	G	K	R	R	H	P	K	K	L	T	P	L	A
mutated	not conserved	31	S	G	L	A	C	G	P	G	R	G	F	R	K	R	R	H	P	K	K	L	T	P	L
Ptroglodytes	all identical	34	S	G	L	A	C	G	P	G	R	G	F	G	K	R	R	H	P	K	K	L	T	P	L
Mmulatta	all identical	34	S	G	L	A	C	G	P	G	R	G	F	G	K	R	R	H	P	K	K	L	T	P	L
Fcatus	no alignment	n/a
Mmusculus	all identical	32	P	G	L	A	C	G	P	G	R	G	F	G	K	R	R	H	P	K	K	L	T	P	L
Ggallus	all identical	34	S	G	L	T	C	G	P	G	R	G	I	G	K	R	R	H	P	K	K	L	T	P	L
Trubripes	all identical	31	S	G	M	G	C	G	P	G	R	G	Y	G	R	R	R	H	P	K	K	L	T	P	L
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no alignment	n/a
Xtropicalis	all identical	31	P	G	L	A	C	G	P	G	R	G	I	G	K	R	R	H	P	K	K	L	T	P	L

Protein features

Start (aa)	End (aa)	Feature
24	197	CHAIN	lost
24	462	CHAIN	lost
30	32	STRAND	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.723	1
	7.723	1
(flanking)	1.306	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

7

Strand

-1

Original gDNA sequence snippet

GCGGACCGGGCAGGGGGTTCGGGAAGAGGAGGCACCCCAAA

Altered gDNA sequence snippet

GCGGACCGGGCAGGGGGTTCAGGAAGAGGAGGCACCCCAAA

Original cDNA sequence snippet

GCGGACCGGGCAGGGGGTTCGGGAAGAGGAGGCACCCCAAA

Altered cDNA sequence snippet

GCGGACCGGGCAGGGGGTTCAGGAAGAGGAGGCACCCCAAA

Wildtype AA sequence

MLLLARCLLL VLVSSLLVCS GLACGPGRGF GKRRHPKKLT PLAYKQFIPN VAEKTLGASG
RYEGKISRNS ERFKELTPNY NPDIIFKDEE NTGADRLMTQ RCKDKLNALA ISVMNQWPGV
KLRVTEGWDE DGHHSEESLH YEGRAVDITT SDRDRSKYGM LARLAVEAGF DWVYYESKAH
IHCSVKAENS VAAKSGGCFP GSATVHLEQG GTKLVKDLSP GDRVLAADDQ GRLLYSDFLT
FLDRDDGAKK VFYVIETREP RERLLLTAAH LLFVAPHNDS ATGEPEASSG SGPPSGGALG
PRALFASRVR PGQRVYVVAE RDGDRRLLPA AVHSVTLSEE AAGAYAPLTA QGTILINRVL
ASCYAVIEEH SWAHRAFAPF RLAHALLAAL APARTDRGGD SGGGDRGGGG GRVALTAPGA
ADAPGAGATA GIHWYSQLLY QIGTWLLDSE ALHPLGMAVK SS*

Mutated AA sequence

MLLLARCLLL VLVSSLLVCS GLACGPGRGF RKRRHPKKLT PLAYKQFIPN VAEKTLGASG
RYEGKISRNS ERFKELTPNY NPDIIFKDEE NTGADRLMTQ RCKDKLNALA ISVMNQWPGV
KLRVTEGWDE DGHHSEESLH YEGRAVDITT SDRDRSKYGM LARLAVEAGF DWVYYESKAH
IHCSVKAENS VAAKSGGCFP GSATVHLEQG GTKLVKDLSP GDRVLAADDQ GRLLYSDFLT
FLDRDDGAKK VFYVIETREP RERLLLTAAH LLFVAPHNDS ATGEPEASSG SGPPSGGALG
PRALFASRVR PGQRVYVVAE RDGDRRLLPA AVHSVTLSEE AAGAYAPLTA QGTILINRVL
ASCYAVIEEH SWAHRAFAPF RLAHALLAAL APARTDRGGD SGGGDRGGGG GRVALTAPGA
ADAPGAGATA GIHWYSQLLY QIGTWLLDSE ALHPLGMAVK SS*

Position of stopcodon in wt / mu CDS

1389 / 1389

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

463 / 463

Position of stopcodon in wt / mu cDNA

1730 / 1730

Position of start ATG in wt / mu cDNA

342 / 342

Last intron/exon boundary

903

Theoretical NMD boundary in CDS

511

Length of CDS

1389

Coding sequence (CDS) position

91

cDNA position

432

gDNA position

432

Chromosomal position

155812032

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

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