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: ENST00000406846
Querying Taster for transcript #2: ENST00000304421
MT speed 0.04 s - this script 2.423465 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
ENST00000406846(MANE Select)	FSHR	Benign	0\|200	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD
ENST00000304421	FSHR	Benign	0\|200	without_aae		No				Single base exchange		N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

2:49039455T>C_1_ENST00000406846

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Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:49039455T>C (GRCh38)

Gene symbol

FSHR

Gene constraints

LOEUF: 1.07, LOF (oe): 0.83, misssense (oe): 1.09, synonymous (oe): 1.23 ? (gnomAD)

Ensembl transcript ID

ENST00000406846.7

Genbank transcript ID

NM_000145 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.225-19295A>G
g.115073A>G

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1277460
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	18441	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.026	0.001
	-1.466	0
(flanking)	-0.718	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

AGCACTGTTGACCTTTGTATACTGCTCTGTGCCCTCCTCCA

Altered gDNA sequence snippet

AGCACTGTTGACCTTTGTATGCTGCTCTGTGCCCTCCTCCA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLD IQDNINIHTI ERNSFVGLSF ESVILWLNKN
GIQEIHNCAF NGTQLDELNL SDNNNLEELP NDVFHGASGP VILDISRTRI HSLPSYGLEN
LKKLRARSTY NLKKLPTLEK LVALMEASLT YPSHCCAFAN WRRQISELHP ICNKSILRQE
VDYMTQARGQ RSSLAEDNES SYSRGFDMTY TEFDYDLCNE VVDVTCSPKP DAFNPCEDIM
GYNILRVLIW FISILAITGN IIVLVILTTS QYKLTVPRFL MCNLAFADLC IGIYLLLIAS
VDIHTKSQYH NYAIDWQTGA GCDAAGFFTV FASELSVYTL TAITLERWHT ITHAMQLDCK
VQLRHAASVM VMGWIFAFAA ALFPIFGISS YMKVSICLPM DIDSPLSQLY VMSLLVLNVL
AFVVICGCYI HIYLTVRNPN IVSSSSDTRI AKRMAMLIFT DFLCMAPISF FAISASLKVP
LITVSKAKIL LVLFHPINSC ANPFLYAIFT KNFRRDFFIL LSKCGCYEMQ AQIYRTETSS
TVHNTHPRNG HCSSAPRVTS GSTYILVPLS HLAQN*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

99 / 99

Last intron/exon boundary

952

Theoretical NMD boundary in CDS

803

Length of CDS

2088

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

115073

Chromosomal position

49039455

Speed

0.02 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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MutationT@ster 2025

Variant:

2:49039455T>C_2_ENST00000304421

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: without_aae
Tree vote: 0|200 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr2:49039455T>C (GRCh38)

Gene symbol

FSHR

Gene constraints

LOEUF: 1.04, LOF (oe): 0.80, misssense (oe): 1.09, synonymous (oe): 1.23 ? (gnomAD)

Ensembl transcript ID

ENST00000304421.8

Genbank transcript ID

NM_181446 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

intron

DNA changes

c.225-19295A>G
g.115073A>G

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1277460
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	>32000	18441	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.026	0.001
	-1.466	0
(flanking)	-0.718	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

N/A

AA sequence altered

N/A

Chromosome

2

Strand

-1

Original gDNA sequence snippet

AGCACTGTTGACCTTTGTATACTGCTCTGTGCCCTCCTCCA

Altered gDNA sequence snippet

AGCACTGTTGACCTTTGTATGCTGCTCTGTGCCCTCCTCCA

Original cDNA sequence snippet

N/A

Altered cDNA sequence snippet

N/A

Wildtype AA sequence

MALLLVSLLA FLSLGSGCHH RICHCSNRVF LCQESKVTEI PSDLPRNAIE LRFVLTKLRV
IQKGAFSGFG DLEKIEISQN DVLEVIEADV FSNLPKLHEI RIEKANNLLY INPEAFQNLP
NLQYLLISNT GIKHLPDVHK IHSLQKVLLW LNKNGIQEIH NCAFNGTQLD ELNLSDNNNL
EELPNDVFHG ASGPVILDIS RTRIHSLPSY GLENLKKLRA RSTYNLKKLP TLEKLVALME
ASLTYPSHCC AFANWRRQIS ELHPICNKSI LRQEVDYMTQ ARGQRSSLAE DNESSYSRGF
DMTYTEFDYD LCNEVVDVTC SPKPDAFNPC EDIMGYNILR VLIWFISILA ITGNIIVLVI
LTTSQYKLTV PRFLMCNLAF ADLCIGIYLL LIASVDIHTK SQYHNYAIDW QTGAGCDAAG
FFTVFASELS VYTLTAITLE RWHTITHAMQ LDCKVQLRHA ASVMVMGWIF AFAAALFPIF
GISSYMKVSI CLPMDIDSPL SQLYVMSLLV LNVLAFVVIC GCYIHIYLTV RNPNIVSSSS
DTRIAKRMAM LIFTDFLCMA PISFFAISAS LKVPLITVSK AKILLVLFHP INSCANPFLY
AIFTKNFRRD FFILLSKCGC YEMQAQIYRT ETSSTVHNTH PRNGHCSSAP RVTSGSTYIL
VPLSHLAQN*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

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

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

65 / 65

Last intron/exon boundary

840

Theoretical NMD boundary in CDS

725

Length of CDS

2010

Coding sequence (CDS) position

N/A

cDNA position

N/A

gDNA position

115073

Chromosomal position

49039455

Speed

0.02 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