MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000329078
MT speed 0.04 s - this script 2.439206 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
ENST00000329078(MANE Select)	SPNS2	Benign	1\|9	complex_aae		No				Deletion		Deletion of more than 2 AA	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

17:4499258CCCCCCGGCA>C_1_ENST00000329078

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: complex_aae
Tree vote: 1|9 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr17:4499259_4499267delCCCCCGGCA (GRCh38)

Gene symbol

SPNS2

Gene constraints

LOEUF: 0.96, LOF (oe): 0.73, misssense (oe): 1.16, synonymous (oe): 1.39 ? (gnomAD)

Ensembl transcript ID

ENST00000329078.8

Genbank transcript ID

NM_001124758 (exact from MANE)

UniProt / AlphaMissense peptide

SPNS2_HUMAN | AlphaMissense: transcript, gene

Variant type

Deletion

Gene region

CDS

DNA changes

c.212_220delCCCCCGGCA
g.379_387delCCCCCGGCA

AA changes

deletion of more than 2 AA

AAE:	P72-	G73-	T74-	?
Score:	-	-	-

Frameshift

No

Length of protein

Deletion of more than 2 AA

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs763007985
gnomAD	homozygous (-/-)	heterozygous	allele carriers
	2	963	965

Protein conservation

Species	Match	AA	Alignment
Human		72	S	G	S	V	R	R	A	P	T	G	P	P	G	T	P	G	T	P	G	C	A	A	T	A	K	G
mutated	all identical	72	S	G	S	V	R	R	A	P	T	G	P	P	G	T	P	G	-	-	-	C	A	A	T	A	K
Ptroglodytes	all identical	72	S	G	S	V	R	R	A	P	T	G	P	P	G	T	P	G	-	-	-	C	A	A	T	A	K
Mmulatta	all identical	72	S	G	S	V	R	R	A	P	T	G	P	P	G	T	P	G	T	P	G	C	A	A	T	A	K
Fcatus	all identical	72	S	G	S	V	R	R	A	P	S	G	P	P	G	T	P	G	T	P	G	C	A	A	A	A	K
Mmusculus	partly conserved	72	S	G	S	V	R	R	V	P	S	G	L	P	S	I	P	S	T	P	G	C	A	A	A	A	K
Ggallus	partly conserved	64	S	G	R	M	N	-	-	-	-	-	P	P	A	V	G	K	R	P	-	-	-	-	-	-	E
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	partly conserved	25								P	P	P	P	Y	T	T	PT	D	S	P	E	D	K	I	R	S	N
Xtropicalis	partly conserved	31	P	G	A	E	E	R	G	L	E	T	L	P	G	R	M	N	P	T	S	LDVK	A	V	E	L	E

Protein features

Start (aa)	End (aa)	Feature	Details
1	549	CHAIN		lost
61	97	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.754	0.999
	1.854	1
	0.334	0.977
	0.331	0.977
	3.545	1
	0.917	1
	1.261	1
	3.655	1
	3.324	0.99
	-0.115	0.269
(flanking)	0.787	0.068

?

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

17

Strand

1

Original gDNA sequence snippet

AAGGCGGGCCCCGACCGGACCCCCCGGCACCCCCGGCACCCCCGGCTGC

Altered gDNA sequence snippet

AAGGCGGGCCCCGACCGGACCCCCCGGCACCCCCGGCTGC

Original cDNA sequence snippet

AAGGCGGGCCCCGACCGGACCCCCCGGCACCCCCGGCACCCCCGGCTGC

Altered cDNA sequence snippet

AAGGCGGGCCCCGACCGGACCCCCCGGCACCCCCGGCTGC

Wildtype AA sequence

MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL
SGSVRRAPTG PPGTPGTPGC AATAKGPGAQ QPKPASLGRG RGAAAAILSL GNVLNYLDRY
TVAGVLLDIQ QHFGVKDRGA GLLQSVFICS FMVAAPIFGY LGDRFNRKVI LSCGIFFWSA
VTFSSSFIPQ QYFWLLVLSR GLVGIGEASY STIAPTIIGD LFTKNTRTLM LSVFYFAIPL
GSGLGYITGS SVKQAAGDWH WALRVSPVLG MITGTLILIL VPATKRGHAD QLGDQLKART
SWLRDMKALI RNRSYVFSSL ATSAVSFATG ALGMWIPLYL HRAQVVQKTA ETCNSPPCGA
KDSLIFGAIT CFTGFLGVVT GAGATRWCRL KTQRADPLVC AVGMLGSAIF ICLIFVAAKS
SIVGAYICIF VGETLLFSNW AITADILMYV VIPTRRATAV ALQSFTSHLL GDAGSPYLIG
FISDLIRQST KDSPLWEFLS LGYALMLCPF VVVLGGMFFL ATALFFVSDR ARAEQQVNQL
AMPPASVKV*

Mutated AA sequence

MMCLECASAA AGGAEEEEAD AERRRRRRGA QRGAGGSGCC GARGAGGAGV SAAGDEVQTL
SGSVRRAPTG PPGTPGCAAT AKGPGAQQPK PASLGRGRGA AAAILSLGNV LNYLDRYTVA
GVLLDIQQHF GVKDRGAGLL QSVFICSFMV AAPIFGYLGD RFNRKVILSC GIFFWSAVTF
SSSFIPQQYF WLLVLSRGLV GIGEASYSTI APTIIGDLFT KNTRTLMLSV FYFAIPLGSG
LGYITGSSVK QAAGDWHWAL RVSPVLGMIT GTLILILVPA TKRGHADQLG DQLKARTSWL
RDMKALIRNR SYVFSSLATS AVSFATGALG MWIPLYLHRA QVVQKTAETC NSPPCGAKDS
LIFGAITCFT GFLGVVTGAG ATRWCRLKTQ RADPLVCAVG MLGSAIFICL IFVAAKSSIV
GAYICIFVGE TLLFSNWAIT ADILMYVVIP TRRATAVALQ SFTSHLLGDA GSPYLIGFIS
DLIRQSTKDS PLWEFLSLGY ALMLCPFVVV LGGMFFLATA LFFVSDRARA EQQVNQLAMP
PASVKV*

Position of stopcodon in wt / mu CDS

1650 / 1641

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

550 / 547

Position of stopcodon in wt / mu cDNA

1817 / 1808

Position of start ATG in wt / mu cDNA

168 / 168

Last intron/exon boundary

1821

Theoretical NMD boundary in CDS

1603

Length of CDS

1650

Coding sequence (CDS) position

211 / 221

cDNA position

378 / 388

gDNA position

378 / 388

Chromosomal position

4499258 / 4499268

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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