This abnormality is called hypospadias. It is a birth defect, that involves an abnormally placed urethral meatus (the urinary opening). The meatus can be located anywhere along the underside of the penile shaft to the scrotum, instead of at the tip of the glans (head).
From the description, it seems like the meatus is near the glans. He may also have a urethral fistula.
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