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: ENST00000641820
Querying Taster for transcript #3: ENST00000641407
Querying Taster for transcript #4: ENST00000423400
Querying Taster for transcript #5: ENST00000376585
Querying Taster for transcript #6: ENST00000376583
Querying Taster for transcript #7: ENST00000376590
MT speed 0.59 s - this script 3.015903 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000376590(MANE Select)	MTHFR	Benign	77\|23	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000423400	MTHFR	Benign	79\|21	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000641407	MTHFR	Benign	80\|20	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD
ENST00000376592	MTHFR	Benign	84\|16	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000376585	MTHFR	Benign	84\|16	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000376583	MTHFR	Benign	84\|16	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000641820	MTHFR	Benign	100\|0	5utr	No	Single base exchange	N/A	Homozygous in gnomAD

MutationT@ster 2025

Variant:

1:11796321G>A_7_ENST00000376590

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 77|23 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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

MTHR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.665C>T
g.10135C>T

AA changes

AAE:	A222V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		222	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	222	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
Ptroglodytes	all identical	222	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A
Mmulatta	all identical	263	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A
Fcatus	all identical	262	L	K	Y	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A
Mmusculus	all identical	262	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A
Ggallus	all identical	224	L	K	H	L	K	E	K	V	L	A	G	A	D	F	I	I	T	Q	L	F	F	R	P
Trubripes	all identical	250	L	R	H	L	K	E	K	V	D	A	G	A	D	F	V	I	T	Q	L	F	F	R	A
Drerio	no homologue
Dmelanogaster	all identical	204	M	E	F	L	K	A	K	I	D	A	G	A	D	C	I	I	T	Q	L	C	Y	R	P
Celegans	all identical	235							K	C	D	A	G	A	N	F	V	I	T	Q	L	F	F	E	A
Xtropicalis	all identical	238	L	K	H	L	K	E	K	V	D	A	G	A	D	F	I	I	T	Q	L	F	F	R	A

Protein features

Start (aa)	End (aa)	Feature	Details
1	656	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GVDFIITQLF 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*

Position of stopcodon in wt / mu CDS

1971 / 1971

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

657 / 657

Position of stopcodon in wt / mu cDNA

2061 / 2061

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

665

cDNA position

755

gDNA position

10135

Chromosomal position

11796321

Speed

0.10 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:

1:11796321G>A_4_ENST00000423400

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 79|21 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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

CDS

DNA changes

c.785C>T
g.10135C>T

AA changes

AAE:	A262V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		262	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	262	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
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)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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

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 GVDFIITQLF 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*

Position of stopcodon in wt / mu CDS

2091 / 2091

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

697 / 697

Position of stopcodon in wt / mu cDNA

2103 / 2103

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

785

cDNA position

797

gDNA position

10135

Chromosomal position

11796321

Speed

0.11 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:

1:11796321G>A_3_ENST00000641407

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD

Model: simple_aae
Tree vote: 80|20 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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.665C>T
g.10135C>T

AA changes

AAE:	A222V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		222	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	222	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
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)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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 GVDFIITQLF 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*

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

665

cDNA position

932

gDNA position

10135

Chromosomal position

11796321

Speed

0.08 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:

1:11796321G>A_1_ENST00000376592

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 84|16 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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

MTHR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.665C>T
g.10135C>T

AA changes

AAE:	A222V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		222	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	222	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
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

Start (aa)	End (aa)	Feature	Details
1	656	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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

MVNEARGNSS LNPCLEGSAS SGSESSKDSS RCSTPGLDPE RHERLREKMR RRLESGDKWF
SLEFFPPRTA EGAVNLISRF DRMAAGGPLY IDVTWHPAGD PGSDKETSSM MIASTAVNYC
GLETILHMTC CRQRLEEITG HLHKAKQLGL KNIMALRGDP IGDQWEEEEG GFNYAVDLVK
HIRSEFGDYF DICVAGYPKG HPEAGSFEAD LKHLKEKVSA GVDFIITQLF 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*

Position of stopcodon in wt / mu CDS

1971 / 1971

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

657 / 657

Position of stopcodon in wt / mu cDNA

3421 / 3421

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

665

cDNA position

2115

gDNA position

10135

Chromosomal position

11796321

Speed

0.09 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:

1:11796321G>A_5_ENST00000376585

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Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 84|16 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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

MTHR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.788C>T
g.10135C>T

AA changes

AAE:	A263V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		263	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	263	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
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

Start (aa)	End (aa)	Feature	Details
1	656	CHAIN		lost
263	272	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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

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 AGVDFIITQL 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*

Position of stopcodon in wt / mu CDS

2094 / 2094

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

698 / 698

Position of stopcodon in wt / mu cDNA

3146 / 3146

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

788

cDNA position

1840

gDNA position

10135

Chromosomal position

11796321

Speed

0.09 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:

1:11796321G>A_6_ENST00000376583

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Homozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 84|16 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (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

MTHR_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.788C>T
g.10135C>T

AA changes

AAE:	A263V	?
Score:	64

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		263	L	K	H	L	K	E	K	V	S	A	G	A	D	F	I	I	T	Q	L	F	F	E	A	D
mutated	not conserved	263	L	K	H	L	K	E	K	V	S	A	G	V	D	F	I	I	T	Q	L	F	F	E	A
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

Start (aa)	End (aa)	Feature	Details
1	656	CHAIN		lost
263	272	HELIX		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

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

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 AGVDFIITQL 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*

Position of stopcodon in wt / mu CDS

2094 / 2094

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

698 / 698

Position of stopcodon in wt / mu cDNA

2094 / 2094

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

788

cDNA position

788

gDNA position

10135

Chromosomal position

11796321

Speed

0.11 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:

1:11796321G>A_2_ENST00000641820

Back to summary table

Prediction:

BenignPermalink

Summary:

Homozygous in gnomAD

Model: 5utr
Tree vote: 100|0 (del | benign) ?
Automatic classification due to gnomAD,
tree vote conflicts with the automatic classification ?

Analysed issue

Analysis result

Variant

Chr1:11796321G>A (GRCh38)

Gene symbol

MTHFR

Gene constraints

LOEUF: 0.96, LOF (oe): 0.73, misssense (oe): 0.80, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000641820.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

5'UTR

DNA changes

cDNA.225C>T
g.10135C>T

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	rs1801133
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	>32000	>32000	>32000

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.005	0.952
	9.137	1
(flanking)	7.205	1

?

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

N/A

Chromosome

1

Strand

-1

Original gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered gDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Original cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGCCGATTTCATCATCACGCAGC

Altered cDNA sequence snippet

GGAGAAGGTGTCTGCGGGAGTCGATTTCATCATCACGCAGC

Wildtype AA sequence

MGITCPIVPG IFPIQGYHSL RQLVKLSKLE VPQEIKDVIE PIKDNDAAIR NYGIELAVSL
CQELLASGLV PGLHFYTLNR EMATTEVLKR LGMWTEDPRR PLPWALSAHP KRREEDVRPI
FWASRPKSYI YRTQEWDEFP NGRWGNSSSP AFGELKDYYL FYLKSKSPKE ELLKMWGEEL
TSEESVFEVF VLYLSGEPNR NGHKVTCLPW NDEPLAAETS LLKEELLRVN RQGILTINSQ
PNINGKPSSD PIVGWGPSGG YVFQKAYLEF FTSRETAEAL LQVLKKYELR VNYHLVNVKG
ENITNAPELQ PNAVTWGIFP GREIIQPTVV DPVSFMFWKD EAFALWIERW GKLYEEESPS
RTIIQYIHDN YFLVNLVDND FPLDNCLWQV VEDTLELLNR PTQNARETEA P*

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

296 / 296

Last intron/exon boundary

1312

Theoretical NMD boundary in CDS

966

Length of CDS

1236

Coding sequence (CDS) position

N/A

cDNA position

225

gDNA position

10135

Chromosomal position

11796321

Speed

0.01 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