MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000392539
MT speed 0.12 s - this script 2.576986 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
ENST00000392539(MANE Select)	HOXD13	Deleterious	92\|8	simple_aae		No	Yes			Single base exchange		Normal	Amino acid sequence changed Known disease mutation: ClinVar ID 14869 (pathogenic) Protein features (might be) affected

MutationT@ster 2025

Variant:

2:176094662A>C_1_ENST00000392539

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Known disease mutation: ClinVar ID 14869 (pathogenic)
Protein features (might be) affected

Model: simple_aae
Tree vote: 92|8 (del | benign) ?
Automatic classification due to ClinVar

Analysed issue

Analysis result

Variant

Chr2:176094662A>C (GRCh38)

Gene symbol

HOXD13

Gene constraints

LOEUF: 0.96, LOF (oe): 0.63, misssense (oe): 1.08, synonymous (oe): 1.21 ? (gnomAD)

Ensembl transcript ID

ENST00000392539.4

Genbank transcript ID

NM_000523 (exact from MANE)

UniProt / AlphaMissense peptide

HXD13_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.964A>C
g.1942A>C

AA changes

AAE:	I322L	?
Score:	5

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Brachydactyly type E
Brachydactyly type D

pathogenic

ClinVar OMIM

Variant DBs

dbSNP ID	rs28928891
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		322	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K	I
mutated	all conserved	322	A	A	T	N	L	S	E	R	Q	V	T	L	W	F	Q	N	R	R	V	K	D	K	K
Ptroglodytes	all identical	323	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K
Mmulatta	all identical	322	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K
Fcatus	all identical	320	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K
Mmusculus	all identical	318	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K
Ggallus	all identical	282	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all identical	279	A	A	T	N	L	S	E	R	Q	V	T	I	W	F	Q	N	R	R	V	K	D	K	K

Protein features

Start (aa)	End (aa)	Feature	Details
1	343	CHAIN		lost
276	335	DNA_BIND	Homeobox	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.446	0.996
	9.325	1
(flanking)	8.017	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

2

Strand

1

Original gDNA sequence snippet

TATCTGAGAGACAAGTGACCATTTGGTTTCAGAACCGAAGA

Altered gDNA sequence snippet

TATCTGAGAGACAAGTGACCCTTTGGTTTCAGAACCGAAGA

Original cDNA sequence snippet

TATCTGAGAGACAAGTGACCATTTGGTTTCAGAACCGAAGA

Altered cDNA sequence snippet

TATCTGAGAGACAAGTGACCCTTTGGTTTCAGAACCGAAGA

Wildtype AA sequence

MSRAGSWDMD GLRADGGGAG GAPASSSSSS VAAAAASGQC RGFLSAPVFA GTHSGRAAAA
AAAAAAAAAA ASGFAYPGTS ERTGSSSSSS SSAVVAARPE APPAKECPAP TPAAAAAAPP
SAPALGYGYH FGNGYYSCRM SHGVGLQQNA LKSSPHASLG GFPVEKYMDV SGLASSSVPA
NEVPARAKEV SFYQGYTSPY QHVPGYIDMV STFGSGEPRH EAYISMEGYQ SWTLANGWNS
QVYCTKDQPQ GSHFWKSSFP GDVALNQPDM CVYRRGRKKR VPYTKLQLKE LENEYAINKF
INKDKRRRIS AATNLSERQV TIWFQNRRVK DKKIVSKLKD TVS*

Mutated AA sequence

MSRAGSWDMD GLRADGGGAG GAPASSSSSS VAAAAASGQC RGFLSAPVFA GTHSGRAAAA
AAAAAAAAAA ASGFAYPGTS ERTGSSSSSS SSAVVAARPE APPAKECPAP TPAAAAAAPP
SAPALGYGYH FGNGYYSCRM SHGVGLQQNA LKSSPHASLG GFPVEKYMDV SGLASSSVPA
NEVPARAKEV SFYQGYTSPY QHVPGYIDMV STFGSGEPRH EAYISMEGYQ SWTLANGWNS
QVYCTKDQPQ GSHFWKSSFP GDVALNQPDM CVYRRGRKKR VPYTKLQLKE LENEYAINKF
INKDKRRRIS AATNLSERQV TLWFQNRRVK DKKIVSKLKD TVS*

Position of stopcodon in wt / mu CDS

1032 / 1032

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

344 / 344

Position of stopcodon in wt / mu cDNA

1202 / 1202

Position of start ATG in wt / mu cDNA

171 / 171

Last intron/exon boundary

951

Theoretical NMD boundary in CDS

730

Length of CDS

1032

Coding sequence (CDS) position

964

cDNA position

1134

gDNA position

1942

Chromosomal position

176094662

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

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