HasMaleMaternalX
A proband variant is assigned the category HasMaleMaternalX if all of the following are true:
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The proband is male.
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The variant is on the X chromosome.
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The variant is hemizygous (non-reference).
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The father's genotype at this variant's position is hemizygous reference.
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The mother's genotype at this variant's position is heterozygous.
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The mother's genotype includes the proband variant's allele.
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The variant's functional annotations include at least one type in maternal_x_functional_types.
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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:
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This category detects possible causative variants inherited from the mother on the single X-chromosome of a male proband (conditions 1 and 2 above).
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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).
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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).
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The variant is detrimental (condition 7).