MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000302392
MT speed 0.16 s - this script 2.610888 s

Transcript summary:

Permalink

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
ENST00000302392(MANE Select)	TMEM42	Benign	21\|79	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

3:44861946C>G_1_ENST00000302392

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 21|79 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:44861946C>G (GRCh38)

Gene symbol

TMEM42

Gene constraints

LOEUF: 1.02, LOF (oe): 0.57, misssense (oe): 1.14, synonymous (oe): 1.37 ? (gnomAD)

Ensembl transcript ID

ENST00000302392.5

Genbank transcript ID

NM_144638 (exact from MANE)

UniProt / AlphaMissense peptide

TMM42_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.22C>G
g.43C>G

AA changes

AAE:	P8A	?
Score:	27

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
gnomAD	homozygous (G/G)	heterozygous	allele carriers
	0	2	2

Protein conservation

Species	Match	AA
Human		8	M	A	E	R	P	G	P	P	G	G	A	V	S	A	T	A	Y	P	D	T
mutated	not conserved	8	M	A	E	R	P	G	P	A	G	G	A	V	S	A	T	A	Y	P	D	T	P	A
Ptroglodytes	all identical	8	M	A	E	R	P	G	P	P	G	G	A	V	S	A	T	A	Y	P	D	T	P	A
Mmulatta	no homologue
Fcatus	all identical	31	M	A	E	R	L	Q	S	P	G	G	A	V	C	P	A	S	Y	P	D	A	P	A
Mmusculus	not conserved	8	M	A	A	G	P	Q	S	S	G	A	A	V	S	A	A	A	Y	P	D	S	P	V
Ggallus	no alignment	n/a
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no alignment	n/a
Celegans	no alignment	n/a
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
1	159	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.291	0
	-0.617	0
(flanking)	-0.629	0

?

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

3

Strand

1

Original gDNA sequence snippet

TGGCCGAGAGGCCGGGGCCTCCGGGCGGCGCCGTGTCCGCG

Altered gDNA sequence snippet

TGGCCGAGAGGCCGGGGCCTGCGGGCGGCGCCGTGTCCGCG

Original cDNA sequence snippet

TGGCCGAGAGGCCGGGGCCTCCGGGCGGCGCCGTGTCCGCG

Altered cDNA sequence snippet

TGGCCGAGAGGCCGGGGCCTGCGGGCGGCGCCGTGTCCGCG

Wildtype AA sequence

MAERPGPPGG AVSATAYPDT PAEFPPHLQA GAMRRRFWGV FNCLCAGAFG ALAAASAKLA
FGSEVSMGLC VLGIIVMAST NSLMWTFFSR GLSFSMSSAI ASVTVTFSNI LSSAFLGYVL
YGECQEVLWW GGVFLILCGL TLIHRKLPPT WKPLPHKQQ*

Mutated AA sequence

MAERPGPAGG AVSATAYPDT PAEFPPHLQA GAMRRRFWGV FNCLCAGAFG ALAAASAKLA
FGSEVSMGLC VLGIIVMAST NSLMWTFFSR GLSFSMSSAI ASVTVTFSNI LSSAFLGYVL
YGECQEVLWW GGVFLILCGL TLIHRKLPPT WKPLPHKQQ*

Position of stopcodon in wt / mu CDS

480 / 480

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

160 / 160

Position of stopcodon in wt / mu cDNA

493 / 493

Position of start ATG in wt / mu cDNA

14 / 14

Last intron/exon boundary

352

Theoretical NMD boundary in CDS

288

Length of CDS

480

Coding sequence (CDS) position

22

cDNA position

35

gDNA position

43

Chromosomal position

44861946

Speed

0.16 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

Back to summary table