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: ENST00000376592
Querying Taster for transcript #2: ENST00000641407
Querying Taster for transcript #3: ENST00000423400
Querying Taster for transcript #4: ENST00000376585
Querying Taster for transcript #5: ENST00000376583
Querying Taster for transcript #6: ENST00000376590
MT speed 0.18 s - this script 2.549024 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000641407	MTHFR	Deleterious	57\|43	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD
ENST00000376585	MTHFR	Benign	0\|100	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000376583	MTHFR	Benign	0\|100	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000376592	MTHFR	Benign	1\|99	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000423400	MTHFR	Benign	1\|99	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD
ENST00000376590(MANE Select)	MTHFR	Benign	1\|99	3utr	No	Single base exchange	N/A	Heterozygous in gnomAD

MutationT@ster 2025

Variant:

1:11790562G>C_2_ENST00000641407

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD

Model: simple_aae
Tree vote: 57|43 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.83, LOF (oe): 0.65, misssense (oe): 0.84, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000641407.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1907C>G
g.15894C>G

AA changes

AAE:	P636R	?
Score:	103

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

Species	Match	AA	Alignment
Human		636	L	L	R	V	S	P	T	P	A	S	T	P	P	P	D	N	G	S	*
mutated	not conserved	636	L	L	R	V	S	P	T	P	A	S	T	R	P	P	D	N	G	S
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GADFIITQLF FEADTFFRFV
KACTDMGITC PIVPGIFPIQ GYHSLRQLVK LSKLEVPQEI KDVIEPIKDN DAAIRNYGIE
LAVSLCQELL ASGLVPGLHF YTLNREMATT EVLKRLGMWT EDPRRPLPWA LSAHPKRREE
DVRPIFWASR PKSYIYRTQE WDEFPNGRWG NSSSPAFGEL KDYYLFYLKS KSPKEELLKM
WGEELTSEES VFEVFVLYLS GEPNRNGHKV TCLPWNDEPL AAETSLLKEE LLRVNRQGIL
TINSQPNING KPSSDPIVGW GPSGGYVFQK AYLEFFTSRE TAEALLQVLK KYELRVNYHL
VNVKGENITN APELQPNAVT WGIFPGREII QPTVVDPVSF MFWKAHPECE RNGGSMTLRP
DALRWSHSCP AFLLHSAASL GNSTLLRVSP TPASTPPPDN GS*

Mutated AA sequence

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GADFIITQLF FEADTFFRFV
KACTDMGITC PIVPGIFPIQ GYHSLRQLVK LSKLEVPQEI KDVIEPIKDN DAAIRNYGIE
LAVSLCQELL ASGLVPGLHF YTLNREMATT EVLKRLGMWT EDPRRPLPWA LSAHPKRREE
DVRPIFWASR PKSYIYRTQE WDEFPNGRWG NSSSPAFGEL KDYYLFYLKS KSPKEELLKM
WGEELTSEES VFEVFVLYLS GEPNRNGHKV TCLPWNDEPL AAETSLLKEE LLRVNRQGIL
TINSQPNING KPSSDPIVGW GPSGGYVFQK AYLEFFTSRE TAEALLQVLK KYELRVNYHL
VNVKGENITN APELQPNAVT WGIFPGREII QPTVVDPVSF MFWKAHPECE RNGGSMTLRP
DALRWSHSCP AFLLHSAASL GNSTLLRVSP TPASTRPPDN GS*

Position of stopcodon in wt / mu CDS

1929 / 1929

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

643 / 643

Position of stopcodon in wt / mu cDNA

2196 / 2196

Position of start ATG in wt / mu cDNA

268 / 268

Last intron/exon boundary

2019

Theoretical NMD boundary in CDS

1701

Length of CDS

1929

Coding sequence (CDS) position

1907

cDNA position

2174

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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

MutationT@ster 2025

Variant:

1:11790562G>C_4_ENST00000376585

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 0|100 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.86, LOF (oe): 0.69, misssense (oe): 0.83, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000376585.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.3264C>G
g.15894C>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	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MDHRKARVLP AGHYCPSLGI WASQVGSVRS SVPPSISRNP AMVNEARGNS SLNPCLEGSA
SSGSESSKDS SRCSTPGLDP ERHERLREKM RRRLESGDKW FSLEFFPPRT AEGAVNLISR
FDRMAAGGPL YIDVTWHPAG DPGSDKETSS MMIASTAVNY CGLETILHMT CCRQRLEEIT
GHLHKAKQLG LKNIMALRGD PIGDQWEEEE GGFNYAVDLV KHIRSEFGDY FDICVAGYPK
GHPEAGSFEA DLKHLKEKVS AGADFIITQL FFEADTFFRF VKACTDMGIT CPIVPGIFPI
QGYHSLRQLV KLSKLEVPQE IKDVIEPIKD NDAAIRNYGI ELAVSLCQEL LASGLVPGLH
FYTLNREMAT TEVLKRLGMW TEDPRRPLPW ALSAHPKRRE EDVRPIFWAS RPKSYIYRTQ
EWDEFPNGRW GNSSSPAFGE LKDYYLFYLK SKSPKEELLK MWGEELTSEE SVFEVFVLYL
SGEPNRNGHK VTCLPWNDEP LAAETSLLKE ELLRVNRQGI LTINSQPNIN GKPSSDPIVG
WGPSGGYVFQ KAYLEFFTSR ETAEALLQVL KKYELRVNYH LVNVKGENIT NAPELQPNAV
TWGIFPGREI IQPTVVDPVS FMFWKDEAFA LWIERWGKLY EEESPSRTII QYIHDNYFLV
NLVDNDFPLD NCLWQVVEDT LELLNRPTQN ARETEAP*

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

1053 / 1053

Last intron/exon boundary

2927

Theoretical NMD boundary in CDS

1824

Length of CDS

2094

Coding sequence (CDS) position

N/A

cDNA position

3264

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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

MutationT@ster 2025

Variant:

1:11790562G>C_5_ENST00000376583

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 0|100 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.86, LOF (oe): 0.69, misssense (oe): 0.83, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000376583.7

Genbank transcript ID

NM_001330358 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2212C>G
g.15894C>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	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MDHRKARVLP AGHYCPSLGI WASQVGSVRS SVPPSISRNP AMVNEARGNS SLNPCLEGSA
SSGSESSKDS SRCSTPGLDP ERHERLREKM RRRLESGDKW FSLEFFPPRT AEGAVNLISR
FDRMAAGGPL YIDVTWHPAG DPGSDKETSS MMIASTAVNY CGLETILHMT CCRQRLEEIT
GHLHKAKQLG LKNIMALRGD PIGDQWEEEE GGFNYAVDLV KHIRSEFGDY FDICVAGYPK
GHPEAGSFEA DLKHLKEKVS AGADFIITQL FFEADTFFRF VKACTDMGIT CPIVPGIFPI
QGYHSLRQLV KLSKLEVPQE IKDVIEPIKD NDAAIRNYGI ELAVSLCQEL LASGLVPGLH
FYTLNREMAT TEVLKRLGMW TEDPRRPLPW ALSAHPKRRE EDVRPIFWAS RPKSYIYRTQ
EWDEFPNGRW GNSSSPAFGE LKDYYLFYLK SKSPKEELLK MWGEELTSEE SVFEVFVLYL
SGEPNRNGHK VTCLPWNDEP LAAETSLLKE ELLRVNRQGI LTINSQPNIN GKPSSDPIVG
WGPSGGYVFQ KAYLEFFTSR ETAEALLQVL KKYELRVNYH LVNVKGENIT NAPELQPNAV
TWGIFPGREI IQPTVVDPVS FMFWKDEAFA LWIERWGKLY EEESPSRTII QYIHDNYFLV
NLVDNDFPLD NCLWQVVEDT LELLNRPTQN ARETEAP*

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

1 / 1

Last intron/exon boundary

1875

Theoretical NMD boundary in CDS

1824

Length of CDS

2094

Coding sequence (CDS) position

N/A

cDNA position

2212

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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

MutationT@ster 2025

Variant:

1:11790562G>C_1_ENST00000376592

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.86, LOF (oe): 0.68, misssense (oe): 0.81, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000376592.6

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.3539C>G
g.15894C>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	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GADFIITQLF FEADTFFRFV
KACTDMGITC PIVPGIFPIQ GYHSLRQLVK LSKLEVPQEI KDVIEPIKDN DAAIRNYGIE
LAVSLCQELL ASGLVPGLHF YTLNREMATT EVLKRLGMWT EDPRRPLPWA LSAHPKRREE
DVRPIFWASR PKSYIYRTQE WDEFPNGRWG NSSSPAFGEL KDYYLFYLKS KSPKEELLKM
WGEELTSEES VFEVFVLYLS GEPNRNGHKV TCLPWNDEPL AAETSLLKEE LLRVNRQGIL
TINSQPNING KPSSDPIVGW GPSGGYVFQK AYLEFFTSRE TAEALLQVLK KYELRVNYHL
VNVKGENITN APELQPNAVT WGIFPGREII QPTVVDPVSF MFWKDEAFAL WIERWGKLYE
EESPSRTIIQ YIHDNYFLVN LVDNDFPLDN CLWQVVEDTL ELLNRPTQNA RETEAP*

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

1451 / 1451

Last intron/exon boundary

3202

Theoretical NMD boundary in CDS

1701

Length of CDS

1971

Coding sequence (CDS) position

N/A

cDNA position

3539

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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

MutationT@ster 2025

Variant:

1:11790562G>C_3_ENST00000423400

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.85, LOF (oe): 0.68, misssense (oe): 0.83, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000423400.7

Genbank transcript ID

NM_001410750 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2221C>G
g.15894C>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	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MDHRKARVLP AGHYCPSLGI WASQVGSVRS SVPPSIRNPA MVNEARGNSS LNPCLEGSAS
SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF SLEFFPPRTA EGAVNLISRF
DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC GLETILHMTC CRQRLEEITG
HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK HIRSEFGDYF DICVAGYPKG
HPEAGSFEAD LKHLKEKVSA GADFIITQLF FEADTFFRFV KACTDMGITC PIVPGIFPIQ
GYHSLRQLVK LSKLEVPQEI KDVIEPIKDN DAAIRNYGIE LAVSLCQELL ASGLVPGLHF
YTLNREMATT EVLKRLGMWT EDPRRPLPWA LSAHPKRREE DVRPIFWASR PKSYIYRTQE
WDEFPNGRWG NSSSPAFGEL KDYYLFYLKS KSPKEELLKM WGEELTSEES VFEVFVLYLS
GEPNRNGHKV TCLPWNDEPL AAETSLLKEE LLRVNRQGIL TINSQPNING KPSSDPIVGW
GPSGGYVFQK AYLEFFTSRE TAEALLQVLK KYELRVNYHL VNVKGENITN APELQPNAVT
WGIFPGREII QPTVVDPVSF MFWKDEAFAL WIERWGKLYE EESPSRTIIQ YIHDNYFLVN
LVDNDFPLDN CLWQVVEDTL ELLNRPTQNA RETEAP*

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

13 / 13

Last intron/exon boundary

1884

Theoretical NMD boundary in CDS

1821

Length of CDS

2091

Coding sequence (CDS) position

N/A

cDNA position

2221

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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

MutationT@ster 2025

Variant:

1:11790562G>C_6_ENST00000376590

Back to summary table

Prediction:

BenignPermalink

Summary:

Heterozygous in gnomAD

Model: 3utr
Tree vote: 1|99 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr1:11790562G>C (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.86, LOF (oe): 0.68, misssense (oe): 0.81, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000376590.9

Genbank transcript ID

NM_005957 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.2179C>G
g.15894C>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	rs775426360
gnomAD	homozygous (C/C)	heterozygous	allele carriers
	0	513	513

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	0.769	0.01
	-0.279	0
(flanking)	-1.48	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

polyA signal ok

AA sequence altered

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered gDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Original cDNA sequence snippet

TCCCACCCCGGCCTCCACTCCCCCACCTGACAATGGCAGCT

Altered cDNA sequence snippet

TCCCACCCCGGCCTCCACTCGCCCACCTGACAATGGCAGCT

Wildtype AA sequence

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GADFIITQLF FEADTFFRFV
KACTDMGITC PIVPGIFPIQ GYHSLRQLVK LSKLEVPQEI KDVIEPIKDN DAAIRNYGIE
LAVSLCQELL ASGLVPGLHF YTLNREMATT EVLKRLGMWT EDPRRPLPWA LSAHPKRREE
DVRPIFWASR PKSYIYRTQE WDEFPNGRWG NSSSPAFGEL KDYYLFYLKS KSPKEELLKM
WGEELTSEES VFEVFVLYLS GEPNRNGHKV TCLPWNDEPL AAETSLLKEE LLRVNRQGIL
TINSQPNING KPSSDPIVGW GPSGGYVFQK AYLEFFTSRE TAEALLQVLK KYELRVNYHL
VNVKGENITN APELQPNAVT WGIFPGREII QPTVVDPVSF MFWKDEAFAL WIERWGKLYE
EESPSRTIIQ YIHDNYFLVN LVDNDFPLDN CLWQVVEDTL ELLNRPTQNA RETEAP*

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

91 / 91

Last intron/exon boundary

1842

Theoretical NMD boundary in CDS

1701

Length of CDS

1971

Coding sequence (CDS) position

N/A

cDNA position

2179

gDNA position

15894

Chromosomal position

11790562

Speed

0.03 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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