civicrm_api3('contact', 'create', ['id'=>123, 'gender'=>'Male'])

function getIdforLabel($entity, $field, $label) {

    $result = civicrm_api3($entity, 'getoptions', ['sequential' => 1, 'field' => $field]);
    if ($result['is_error']) {
      throw new Exception("Failed to getoptions for $entity.$field");
    }
    foreach ($result['values'] as $result) {
      if ($result['value'] == $label) {
        return $result['key'];
      }
    }
    throw new Exception("Supplied value, '$label' is not a valid option.");
}

$gender_id = getIdForLabel('contact', 'gender_id', 'Male');
civicrm_api3('contact', 'create', ['id'=>$contact_id, 'gender_id'=>$gender_id]);