NM_005957.5:c.665C>A

Variant names:

• chr1-11796321-G-T
• rs1801133
• NM_005957.5:c.665C>A
• MTHFR p.Ala222Asp

GermlineCancer (beta)

Variant summary

Our verdict is Likely pathogenic.

+6 Likely Pathogenic

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 6 classification points (ACMG Germline Pathogenicity v2019). PM1PM2PP3_Moderate

The NM_005957.5(MTHFR):c.665C>A (p.Ala222Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely damaging/oncogenic. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 9.14). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.A222= (synonymous): Likely_benign (ClinVar VariationId 1658853, 1 star); p.A222V: Likely_benign (ClinVar VariationId 2194685, 1 star); p.A222V: drug_response (ClinVar VariationId 3520, 3 stars)

• Frequency: Genomes: not found (cov: 32)
• Consequence: MTHFR NM_005957.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.14
• Publications: 1 publications found

Genes affected

MTHFR (HGNC:7436): (methylenetetrahydrofolate reductase) The protein encoded by this gene catalyzes the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a co-substrate for homocysteine remethylation to methionine. Genetic variation in this gene influences susceptibility to occlusive vascular disease, neural tube defects, colon cancer and acute leukemia, and mutations in this gene are associated with methylenetetrahydrofolate reductase deficiency.[provided by RefSeq, Oct 2009]

MTHFR Gene-Disease associations (from GenCC):

• homocystinuria due to methylene tetrahydrofolate reductase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Natera, PanelApp Australia, Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Likely_pathogenic. The variant received 6 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM1Mutational hot spot or critical domain		Missense neighbourhood hotspot (≥2 P/LP within ±8 AA, OR ≥ 5 vs. background) — PM1; In-domain: 0 pathogenic, 0 benign rare missense variants.; ±8 AA neighbourhood: 3 pathogenic, 1 benign (OR vs. background: 11.7).
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: AR) (threshold 0.001) — PM2 moderate.
	PP3Computational evidence supports damaging effect		Germline meta computational scorer (REVEL/MetaRNN/BayesDel) predicts damaging effect — moderate evidence (PP3); Splicing verdict: not pathogenic.; Germline computational verdict: pathogenic (Moderate).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_005957.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	MTHFR NM_005957.5	MANE Select	c.665C>A p.Ala222Asp	missense	Exon 5 of 12	Prot: NP_005948.3
	MTHFR NM_001330358.2		c.788C>A p.Ala263Asp	missense	Exon 5 of 12	Prot: NP_001317287.1 UniProt:
	MTHFR NM_001410750.1		c.785C>A p.Ala262Asp	missense	Exon 5 of 12	Prot: NP_001397679.1 UniProt:

MTHFR NM_005957.5

MANE Select

HGVSc / HGVSpc.665C>Ap.Ala222Asp

Exon rankExon 5 of 12

missense

Prot: NP_005948.3

MTHFR NM_001330358.2

HGVSc / HGVSpc.788C>Ap.Ala263Asp

Exon rankExon 5 of 12

missense

Prot: NP_001317287.1UniProt: P42898-2

MTHFR NM_001410750.1

HGVSc / HGVSpc.785C>Ap.Ala262Asp

Exon rankExon 5 of 12

missense

Prot: NP_001397679.1UniProt: Q5SNW7

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	MTHFR ENST00000376590.9	TSL:1MANE Select	c.665C>A p.Ala222Asp	missense	Exon 5 of 12	Prot: ENSP00000365775.3 UniProt:
	MTHFR ENST00000423400.7	TSL:1	c.785C>A p.Ala262Asp	missense	Exon 5 of 12	Prot: ENSP00000398908.3 UniProt:
	MTHFR ENST00000376592.6	TSL:1	c.665C>A p.Ala222Asp	missense	Exon 5 of 12	Prot: ENSP00000365777.1 UniProt:

MTHFR ENST00000376590.9

TSL:1MANE Select

HGVSc / HGVSpc.665C>Ap.Ala222Asp

Exon rankExon 5 of 12

missense

Prot: ENSP00000365775.3UniProt: P42898-1

MTHFR ENST00000423400.7

TSL:1

HGVSc / HGVSpc.785C>Ap.Ala262Asp

Exon rankExon 5 of 12

missense

Prot: ENSP00000398908.3UniProt: Q5SNW7

MTHFR ENST00000376592.6

TSL:1

HGVSc / HGVSpc.665C>Ap.Ala222Asp

Exon rankExon 5 of 12

missense

Prot: ENSP00000365777.1UniProt: P42898-1

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:40
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	30
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.98	D
Eigen	Pathogenic	0.94
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.98	D
FuncVEP CTI	Pathogenic	0.94
GPN-Star LLR	N/A	-8.8
GPN-Star score	N/A	8.8
LIST_S2	Uncertain	0.96	D
M_CAP	Pathogenic	0.44	D
MetaRNN	Pathogenic	0.94	D
MetaSVM	Pathogenic	1.1	D
Mutation Taster	N/A	14/86	disease causing
MutationAssessor	Pathogenic	4.9	H
PhyloP100	Pathogenic	9.1
popEVE	Benign	-4.3
PrimateAI	Uncertain	0.69	T
PromoterAI	N/A	0.034	Neutral
PROVEAN	Pathogenic	-5.0	D
RBP_binding_hub_radar	N/A	0.0
RBP_regulation_power_radar	N/A	1.7
REVEL	Pathogenic	0.92
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0030	D
Varity_R	N/A	0.99
VESM-3B	Benign	-15

Showing 31 of 31 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

7 no calibration

7 assays found for this variant.

No calibration: 7 assays (score only).

None of these data are clinically calibrated — they are not validated, so interpret them with great caution.

Protein level

MTHFR at 100ug/ml folate in A222V background

MTHFR DMS

• Gene: MTHFR
• Score: 0.303 · p.Val222Asp (assay numbering)

No calibration data

This score is at approximately the 19th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 25ug/ml folate in A222V background

MTHFR DMS

• Gene: MTHFR
• Score: 0.0137 · p.Val222Asp (assay numbering)

No calibration data

This score is at approximately the 3th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 25ug/ml folate in WT background

MTHFR DMS

• Gene: MTHFR
• Score: 0.0188 · p.Ala222Asp (assay numbering)

No calibration data

This score is at approximately the 3th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 12ug/ml folate in WT background

MTHFR DMS

• Gene: MTHFR
• Score: 0.0212 · p.Ala222Asp (assay numbering)

No calibration data

This score is at approximately the 4th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 12ug/ml folate in A222V background

MTHFR DMS

• Gene: MTHFR
• Score: 0.00490 · p.Val222Asp (assay numbering)

No calibration data

This score is at approximately the 1th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 200ug/ml folate in WT background

MTHFR DMS

• Gene: MTHFR
• Score: 0.00 · p.Ala222Asp (assay numbering)

No calibration data

This score is at or below the 1st percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Protein level

MTHFR at 100ug/ml folate in WT background

MTHFR DMS

• Gene: MTHFR
• Score: 0.0226 · p.Ala222Asp (assay numbering)

No calibration data

This score is at approximately the 3th percentile of all variants tested in this assay.

This score has not been calibrated against ACMG evidence — shown for context only, not as clinical evidence.

Other links and lift over

dbSNP: rs1801133;

hg19: chr1-11856378;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar