GenVue Discovery

Variant Report

Curation

Conditions reviewed by experts

Below are conditions that were reviewed by an expert panel and/or are in the Genetic Testing Registry (GTR) according to ClinVar. The data presented does not diagnose disease and has no guarantees of reporting accuracy. We report heterozygous variants as yellow and homozygous variants as red. A red or yellow variant does not necessarily mean one has or carries a condition or disease. This is for research and educational purposes only.

Gene: MTHFR
Variant: c.1286A>C
(p.Glu429Ala)
 rsID: rs1801131
Ref Allele: T
Alt Allele: G
Freq: 24.9092%
CADD: 19.91

ClinVar Submissions (6)

  • Gastrointestinal stroma tumor

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

  • MTHFR deficiency, thermolabile type

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

  • Neural tube defects, folate-sensitive

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

  • Schizophrenia, susceptibility to

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

  • not provided

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

  • not specified

    View Clinvar Submission

    Variant Details

    Last Evaluated: May 02, 2017
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other, risk factor
    Assembly: GRCh38
    Chromosome/Position: 1:11794419
    OMIM Allelic Variant: 607093.0004

Expert Reviewed Conflicting/Uncertain

Homo
GG

Gene: CCDC170
Variant: g.151627231G>A
 rsID: rs2046210
Ref Allele: G
Alt Allele: A
Freq: 42.4017%
CADD: 0.277

ClinVar Submissions (1)

  • Estrogen resistance

    Estrogen resistance (ESTRR) is characterized by absence of puberty with elevated estradiol and gonadotropic hormones, as well as markedly delayed bone maturation. Female patients show absent breast development, small uterus, and enlarged multicystic ovaries; male patients may show small testes (Bernard et al., 2017). Some patients exhibit continued growth into adulthood (Smith et al., 1994).

    View Clinvar Submission

    Variant Details

    Last Evaluated: Mar 01, 2014
    Review Status: no assertion criteria provided
    Number of Submitters: 1
    Clinical Significance: Likely pathogenic
    Assembly: GRCh38
    Chromosome/Position: 6:151627231

Expert Reviewed Clinically Significant Likely pathogenic

Hetero
GA

Gene: GALT
Variant: c.940A>G
(p.Asn314Asp)
 rsID: rs2070074
Ref Allele: A
Alt Allele: G
Freq: 6.6665%
CADD: 20.3

ClinVar Submissions (13)

  • Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • GALT POLYMORPHISM (DUARTE, D2)

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • GALT POLYMORPHISM (LOS ANGELES, D1)

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • Galactosemia

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • not provided

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

  • not specified

    View Clinvar Submission

    Variant Details

    Last Evaluated: Feb 13, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 13
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 9:34649445
    OMIM Allelic Variant: 606999.0005

Low clinical importance, Uncertain benign — This variant has an allele frequency of ~8% and is ancestral to "Duarte" / "Duarte 2" and "Duarte 1"/"Los Angeles" galactosemia variants. This variant is evolutionarily ancestral, and in vitro studies fail to support an impact of this variant on enzyme activity. Carney et al. instead implicate a 4 base deletion on the 5' of the GALT gene as being causal and linked to this variant. Galactosemia is typically screened and detected in infants and causes early, severe but nonspecific symptoms (digestive problems, lethargy, failure to thrive).

Expert Reviewed Clinically Significant Conflicting/Uncertain

Hetero
AG

Gene: GALT
Variant: c.652C>T
(p.Leu218=)
 rsID: rs2070075
Ref Allele: C
Alt Allele: T
Freq: 2.2888%uncommon
CADD: 15.26

ClinVar Submissions (9)

  • Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 11, 2017
    Review Status: criteria provided, multiple submitters, no conflicts
    Number of Submitters: 9
    Clinical Significance: Benign/Likely benign, other
    Assembly: GRCh38
    Chromosome/Position: 9:34648421
    OMIM Allelic Variant: 606999.0012

  • GALT POLYMORPHISM (LOS ANGELES, D1)

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 11, 2017
    Review Status: criteria provided, multiple submitters, no conflicts
    Number of Submitters: 9
    Clinical Significance: Benign/Likely benign, other
    Assembly: GRCh38
    Chromosome/Position: 9:34648421
    OMIM Allelic Variant: 606999.0012

  • Galactosemia

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 11, 2017
    Review Status: criteria provided, multiple submitters, no conflicts
    Number of Submitters: 9
    Clinical Significance: Benign/Likely benign, other
    Assembly: GRCh38
    Chromosome/Position: 9:34648421
    OMIM Allelic Variant: 606999.0012

  • not provided

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 11, 2017
    Review Status: criteria provided, multiple submitters, no conflicts
    Number of Submitters: 9
    Clinical Significance: Benign/Likely benign, other
    Assembly: GRCh38
    Chromosome/Position: 9:34648421
    OMIM Allelic Variant: 606999.0012

Expert Reviewed Benign/Likely benign, other

Hetero
CT

Gene: LCT;MCM6
Variant: c.-13907C>T
 rsID: rs4988235
Ref Allele: G
Alt Allele: A
Freq: 38.7662%
CADD: 10.75

ClinVar Submissions (1)

  • Lactase persistence

    View Clinvar Submission

    Variant Details

    Last Evaluated: Nov 20, 2018
    Review Status: no assertion criteria provided
    Number of Submitters: 1
    Clinical Significance: association
    Assembly: GRCh38
    Chromosome/Position: 2:135851076
    OMIM Allelic Variant: 601806.0001

Expert Reviewed

Hetero
GA

Gene: AMPD1
Variant: c.133C>T
(p.Gln45Ter)
 rsID: rs17602729
Ref Allele: G
Alt Allele: A
Freq: 8.0697%
CADD: 36

ClinVar Submissions (6)

  • Muscle AMP deaminase deficiency

    Myoadenylate deaminase deficiency (MMDD) is an autosomal recessive condition that can manifest as exercise-induced muscle pain, occasionally associated with rhabdomyolysis and/or increased serum creatine kinase, or even infantile hypotonia. However, the finding of homozygous mutations among asymptomatic individuals have suggested to some (e.g., Verzijl et al., 1998) that AMPD1 deficiency may be a harmless entity (summary by Castro-Gago et al., 2011). Genetta et al. (2001) stated that AMPD1 deficiency is the most prevalent genetic disease in humans, the number of people heterozygous approaching 10% of Caucasians and individuals of African descent (Sabina et al., 1989). A small percentage of homozygous-deficient individuals, approximately 1.8% of the population, display symptoms of chronic fatigue and lost productivity as well as a predisposition to stress-related ailments, including heart disease and stroke, according to Genetta et al. (2001).

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 27, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 1:114693436
    OMIM Allelic Variant: 102770.0001

  • not provided

    The term 'not provided' is registered in MedGen to support identification of submissions to ClinVar for which no condition was named when assessing the variant. 'not provided' differs from 'not specified', which is used when a variant is asserted to be benign, likely benign, or of uncertain significance for conditions that have not been specified.

    View Clinvar Submission

    Variant Details

    Last Evaluated: Jun 27, 2018
    Review Status: criteria provided, conflicting interpretations
    Number of Submitters: 6
    Clinical Significance: Conflicting interpretations of pathogenicity, other
    Assembly: GRCh38
    Chromosome/Position: 1:114693436
    OMIM Allelic Variant: 102770.0001

Low clinical importance, Likely pathogenic — Causes Adenosine Deaminase Deficiency in a recessive manner. Most of the time individuals do not report symptoms, but when symptoms do exist they to be post-exercise symptoms of muscle weakness, muscle pain, and getting tired more quickly.

Expert Reviewed Clinically Significant Conflicting/Uncertain

Homo
AA