A proband variant is assigned the category HasMaleMaternalX if all of the following are true:

  • The proband is male.

  • The variant is on the X chromosome.

  • The variant is hemizygous (non-reference).

  • The father's genotype at this variant's position is hemizygous reference.

  • The mother's genotype at this variant's position is heterozygous.

  • The mother's genotype includes the proband variant's allele.

  • The variant's functional annotations include at least one type in maternal_x_functional_types.

  • The frequency of the proband's allele is less than maternal_x_max_population_allele_frequency.

The following explain why these conditions apply to this category:

  • This category detects possible causative variants inherited from the mother on the single X-chromosome of a male proband (conditions 1 and 2 above).

  • The father is not affected, so when a variant is causative, the father, with only one X-chromosome, cannot also have that variant at this position (condition 4).

  • If the variant is de novo, it is assigned the categoryHasDeNovoNofRefAllele. For the category HasMaleMaternalX, a variant allele is inherited from the unaffected mother (conditions 5 and 6).

  • The variant is detrimental (condition 7).