MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000301327
MT speed 0.34 s - this script 2.794619 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
ENST00000301327(MANE Select)	MFSD3	Deleterious	67\|33	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

8:144509448C>T_1_ENST00000301327

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 67|33 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr8:144509448C>T (GRCh38)

Gene symbol

MFSD3

Gene constraints

LOEUF: 1.79, LOF (oe): 1.38, misssense (oe): 1.52, synonymous (oe): 1.59 ? (gnomAD)

Ensembl transcript ID

ENST00000301327.5

Genbank transcript ID

NM_138431 (exact from MANE)

UniProt / AlphaMissense peptide

MFSD3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.115C>T
g.379C>T

AA changes

AAE:	R39C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1264241936
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		39	V	L	L	R	A	G	G	L	S	L	T	R	V	G	L	A	K	V	L	Y	A	P	W	L
mutated	not conserved	39	V	L	L	R	A	G	G	L	S	L	T	C	V	G	L	A	K	V	L	Y	A	P	W
Ptroglodytes	all identical	39	V	L	L	R	A	G	G	L	S	L	T	R	V	G	L	A	K	V	L	Y	A	P	W
Mmulatta	no homologue
Fcatus	all identical	39	V	L	L	R	A	R	G	L	S	L	T	R	V	G	L	A	K	V	L	Y	L	P	W
Mmusculus	all identical	39	I	L	L	R	A	R	G	L	S	L	T	R	V	G	L	T	K	G	L	Y	A	P	W
Ggallus	no homologue
Trubripes	all identical	39	V	Y	L	R	G	A	G	Q	S	L	T	R	I	G	F	T	K	I	L	Y	F	P	W
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	39	V	L	L	R	T	K	G	L	S	L	S	H	I	G	L	T	R	I	L	Y	L	P	W

Protein features

Start (aa)	End (aa)	Feature	Details
1	412	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-1.255	0.018
	3.218	0.975
(flanking)	2.493	0.981

?

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

8

Strand

1

Original gDNA sequence snippet

CCGGCGGCCTCTCGCTGACGCGCGTGGGGCTGGCCAAGGTT

Altered gDNA sequence snippet

CCGGCGGCCTCTCGCTGACGTGCGTGGGGCTGGCCAAGGTT

Original cDNA sequence snippet

CCGGCGGCCTCTCGCTGACGCGCGTGGGGCTGGCCAAGGTT

Altered cDNA sequence snippet

CCGGCGGCCTCTCGCTGACGTGCGTGGGGCTGGCCAAGGTT

Wildtype AA sequence

MRGKLLPLAG LYLVQGLPYG LQSGLLPVLL RAGGLSLTRV GLAKVLYAPW LLKLAWAPLV
DAQGSARAWV TRSTAGLGLV CGLLAGLPPP GAGQAGLPAA VAGLLLLLNL GAAMQDVALD
ALAVQLLEPA ELGPGNTVQV VAYKLGAALA GGALLALLPT FSWPQLFLLL AATYWLAAAL
AWAAPALRRL PQQPPSEQRP HTAHLLRDVL AVPGTVWTAG FVLTYKLGEQ GASSLFPLLL
LDHGVSAPEL GLWNGVGAVV CSIAGSSLGG TLLAKHWKLL PLLRSVLRFR LGGLACQTAL
VFHLDTLGAS MDAGTILRGS ALLSLCLQHF LGGLVTTVTF TGMMRCSQLA PRALQATHYS
LLATLELLGK LLLGTLAGGL ADGLGPHPCF LLLLILSAFP VLYLDLAPST FL*

Mutated AA sequence

MRGKLLPLAG LYLVQGLPYG LQSGLLPVLL RAGGLSLTCV GLAKVLYAPW LLKLAWAPLV
DAQGSARAWV TRSTAGLGLV CGLLAGLPPP GAGQAGLPAA VAGLLLLLNL GAAMQDVALD
ALAVQLLEPA ELGPGNTVQV VAYKLGAALA GGALLALLPT FSWPQLFLLL AATYWLAAAL
AWAAPALRRL PQQPPSEQRP HTAHLLRDVL AVPGTVWTAG FVLTYKLGEQ GASSLFPLLL
LDHGVSAPEL GLWNGVGAVV CSIAGSSLGG TLLAKHWKLL PLLRSVLRFR LGGLACQTAL
VFHLDTLGAS MDAGTILRGS ALLSLCLQHF LGGLVTTVTF TGMMRCSQLA PRALQATHYS
LLATLELLGK LLLGTLAGGL ADGLGPHPCF LLLLILSAFP VLYLDLAPST FL*

Position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

Position of stopcodon in wt / mu cDNA

1503 / 1503

Position of start ATG in wt / mu cDNA

265 / 265

Last intron/exon boundary

1329

Theoretical NMD boundary in CDS

1014

Length of CDS

1239

Coding sequence (CDS) position

115

cDNA position

379

gDNA position

379

Chromosomal position

144509448

Speed

0.34 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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