MutationT@ster 2025

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Querying Taster for transcript #1: ENST00000306077
MT speed 0.06 s - this script 2.459206 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
ENST00000306077(MANE Select)	TMEM43	Benign	46\|54	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

3:14130939G>A_1_ENST00000306077

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 46|54 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:14130939G>A (GRCh38)

Gene symbol

TMEM43

Gene constraints

LOEUF: 1.13, LOF (oe): 0.88, misssense (oe): 0.98, synonymous (oe): 0.91 ? (gnomAD)

Ensembl transcript ID

ENST00000306077.5

Genbank transcript ID

NM_024334 (exact from MANE), NM_001407274 (by similarity), NM_001407276 (by similarity), NM_001407275 (by similarity), NM_001407277 (by similarity), NM_001407279 (by similarity), NM_001407278 (by similarity), NM_001407280 (by similarity)

UniProt / AlphaMissense peptide

TMM43_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.280G>A
g.5925G>A

AA changes

AAE:	A94T	?
Score:	58

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs369142200
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	32	32

Protein conservation

Species	Match	AA	Alignment
Human		94	E	N	E	G	R	L	V	H	I	I	G	A	L	R	T	S	K	L	L	S	D	P	N	Y
mutated	not conserved	94	E	N	E	G	R	L	V	H	I	I	G	T	L	R	T	S	K	L	L	S	D	P	N
Ptroglodytes	all identical	94	E	N	E	G	R	L	V	H	I	I	G	A	L	R	T	S	K	L	L	S	D	P	N
Mmulatta	all identical	94	E	N	E	G	R	L	V	H	I	I	G	A	L	R	T	S	K	L	L	S	D	P	N
Fcatus	all identical	94	E	N	E	G	R	L	V	H	I	I	G	A	L	R	T	S	K	L	L	S	D	P	N
Mmusculus	all identical	94	E	N	E	G	R	L	V	H	I	I	G	A	L	R	T	S	K	L	L	S	D	P	N
Ggallus	all identical	94	Q	N	E	G	R	L	V	H	L	A	G	A	L	S	T	A	K	P	L	F	D	P	S
Trubripes	not conserved	95	Q	N	N	N	H	L	V	H	L	F	A	Q	L	K	T	A	Q	P	L	H	D	P	N
Drerio	no homologue
Dmelanogaster	not conserved	73	V	GL	E	G	R	I	V	H	L	S	G	P	I	L	V
Celegans	no homologue
Xtropicalis	all identical	92	Q	N	E	A	N	L	V	H	L	S	G	A	L	R	T	S	K	P	L	Y	D	P	N

Protein features

Start (aa)	End (aa)	Feature	Details
2	400	CHAIN		lost
53	313	TOPO_DOM	Perinuclear space	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.404	0.595
	1.268	0.962
(flanking)	4.028	0.993

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

18

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

1

Original gDNA sequence snippet

GGCTGGTGCACATCATTGGCGCCTTACGGACATCCAAGGTA

Altered gDNA sequence snippet

GGCTGGTGCACATCATTGGCACCTTACGGACATCCAAGGTA

Original cDNA sequence snippet

GGCTGGTGCACATCATTGGCGCCTTACGGACATCCAAGCTT

Altered cDNA sequence snippet

GGCTGGTGCACATCATTGGCACCTTACGGACATCCAAGCTT

Wildtype AA sequence

MAANYSSTST RREHVKVKTS SQPGFLERLS ETSGGMFVGL MAFLLSFYLI FTNEGRALKT
ATSLAEGLSL VVSPDSIHSV APENEGRLVH IIGALRTSKL LSDPNYGVHL PAVKLRRHVE
MYQWVETEES REYTEDGQVK KETRYSYNTE WRSEIINSKN FDREIGHKNP SAMAVESFMA
TAPFVQIGRF FLSSGLIDKV DNFKSLSLSK LEDPHVDIIR RGDFFYHSEN PKYPEVGDLR
VSFSYAGLSG DDPDLGPAHV VTVIARQRGD QLVPFSTKSG DTLLLLHHGD FSAEEVFHRE
LRSNSMKTWG LRAAGWMAMF MGLNLMTRIL YTLVDWFPVF RDLVNIGLKA FAFCVATSLT
LLTVAAGWLF YRPLWALLIA GLALVPILVA RTRVPAKKLE *

Mutated AA sequence

MAANYSSTST RREHVKVKTS SQPGFLERLS ETSGGMFVGL MAFLLSFYLI FTNEGRALKT
ATSLAEGLSL VVSPDSIHSV APENEGRLVH IIGTLRTSKL LSDPNYGVHL PAVKLRRHVE
MYQWVETEES REYTEDGQVK KETRYSYNTE WRSEIINSKN FDREIGHKNP SAMAVESFMA
TAPFVQIGRF FLSSGLIDKV DNFKSLSLSK LEDPHVDIIR RGDFFYHSEN PKYPEVGDLR
VSFSYAGLSG DDPDLGPAHV VTVIARQRGD QLVPFSTKSG DTLLLLHHGD FSAEEVFHRE
LRSNSMKTWG LRAAGWMAMF MGLNLMTRIL YTLVDWFPVF RDLVNIGLKA FAFCVATSLT
LLTVAAGWLF YRPLWALLIA GLALVPILVA RTRVPAKKLE *

Position of stopcodon in wt / mu CDS

1203 / 1203

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

401 / 401

Position of stopcodon in wt / mu cDNA

1345 / 1345

Position of start ATG in wt / mu cDNA

143 / 143

Last intron/exon boundary

1142

Theoretical NMD boundary in CDS

949

Length of CDS

1203

Coding sequence (CDS) position

280

cDNA position

422

gDNA position

5925

Chromosomal position

14130939

Speed

0.06 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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