MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000264079
MT speed 0.05 s - this script 2.499225 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
ENST00000264079(MANE Select)	MCOLN1	Deleterious	86\|14	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

19:7529689G>A_1_ENST00000264079

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 86|14 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr19:7529689G>A (GRCh38)

Gene symbol

MCOLN1

Gene constraints

LOEUF: 0.90, LOF (oe): 0.70, misssense (oe): 0.72, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000264079.11

Genbank transcript ID

NM_020533 (exact from MANE)

UniProt / AlphaMissense peptide

MCLN1_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1336G>A
g.7066G>A

AA changes

AAE:	V446M	?
Score:	21

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs754097561
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA	Alignment
Human		446	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L	S
mutated	all conserved	446	I	Y	L	G	Y	C	F	C	G	W	I	M	L	G	P	Y	H	V	K	F	R	S	L
Ptroglodytes	all identical	467	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L
Mmulatta	all identical	575	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L
Fcatus	all identical	443	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L
Mmusculus	all identical	446	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L
Ggallus	all identical	431	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S	L
Trubripes	all identical	431	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	S
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	all conserved	481	L	Y	A	G	F	L	I	A	G	W	V	I	I	G	P	Y	S	M	K	F	R	T	L
Xtropicalis	all identical	431	I	Y	L	G	Y	C	F	C	G	W	I	V	L	G	P	Y	H	V	K	F	R	T	L

Protein features

Start (aa)	End (aa)	Feature	Details
1	580	CHAIN		lost
409	447	HELIX		lost
428	448	TRANSMEM	Helical	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.898	0.013
	9.602	1
(flanking)	7.674	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

24

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

19

Strand

1

Original gDNA sequence snippet

ACTGCTTCTGTGGCTGGATCGTGCTGGGGCCCTATCATGTG

Altered gDNA sequence snippet

ACTGCTTCTGTGGCTGGATCATGCTGGGGCCCTATCATGTG

Original cDNA sequence snippet

ACTGCTTCTGTGGCTGGATCGTGCTGGGGCCCTATCATGTG

Altered cDNA sequence snippet

ACTGCTTCTGTGGCTGGATCATGCTGGGGCCCTATCATGTG

Wildtype AA sequence

MTAPAGPRGS ETERLLTPNP GYGTQAGPSP APPTPPEEED LRRRLKYFFM SPCDKFRAKG
RKPCKLMLQV VKILVVTVQL ILFGLSNQLA VTFREENTIA FRHLFLLGYS DGADDTFAAY
TREQLYQAIF HAVDQYLALP DVSLGRYAYV RGGGDPWTNG SGLALCQRYY HRGHVDPAND
TFDIDPMVVT DCIQVDPPER PPPPPSDDLT LLESSSSYKN LTLKFHKLVN VTIHFRLKTI
NLQSLINNEI PDCYTFSVLI TFDNKAHSGR IPISLETQAH IQECKHPSVF QHGDNSFRLL
FDVVVILTCS LSFLLCARSL LRGFLLQNEF VGFMWRQRGR VISLWERLEF VNGWYILLVT
SDVLTISGTI MKIGIEAKNL ASYDVCSILL GTSTLLVWVG VIRYLTFFHN YNILIATLRV
ALPSVMRFCC CVAVIYLGYC FCGWIVLGPY HVKFRSLSMV SECLFSLING DDMFVTFAAM
QAQQGRSSLV WLFSQLYLYS FISLFIYMVL SLFIALITGA YDTIKHPGGA GAEESELQAY
IAQCQDSPTS GKFRRGSGSA CSLLCCCGRD PSEEHSLLVN *

Mutated AA sequence

MTAPAGPRGS ETERLLTPNP GYGTQAGPSP APPTPPEEED LRRRLKYFFM SPCDKFRAKG
RKPCKLMLQV VKILVVTVQL ILFGLSNQLA VTFREENTIA FRHLFLLGYS DGADDTFAAY
TREQLYQAIF HAVDQYLALP DVSLGRYAYV RGGGDPWTNG SGLALCQRYY HRGHVDPAND
TFDIDPMVVT DCIQVDPPER PPPPPSDDLT LLESSSSYKN LTLKFHKLVN VTIHFRLKTI
NLQSLINNEI PDCYTFSVLI TFDNKAHSGR IPISLETQAH IQECKHPSVF QHGDNSFRLL
FDVVVILTCS LSFLLCARSL LRGFLLQNEF VGFMWRQRGR VISLWERLEF VNGWYILLVT
SDVLTISGTI MKIGIEAKNL ASYDVCSILL GTSTLLVWVG VIRYLTFFHN YNILIATLRV
ALPSVMRFCC CVAVIYLGYC FCGWIMLGPY HVKFRSLSMV SECLFSLING DDMFVTFAAM
QAQQGRSSLV WLFSQLYLYS FISLFIYMVL SLFIALITGA YDTIKHPGGA GAEESELQAY
IAQCQDSPTS GKFRRGSGSA CSLLCCCGRD PSEEHSLLVN *

Position of stopcodon in wt / mu CDS

1743 / 1743

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

581 / 581

Position of stopcodon in wt / mu cDNA

1870 / 1870

Position of start ATG in wt / mu cDNA

128 / 128

Last intron/exon boundary

1833

Theoretical NMD boundary in CDS

1655

Length of CDS

1743

Coding sequence (CDS) position

1336

cDNA position

1463

gDNA position

7066

Chromosomal position

7529689

Speed

0.05 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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